Hello thank you for your response

I make first below query:

 ;with cte (
 invId, uid, mark, counter_id, counter_vatNumber, counter_country,
 counter_branch, counter_name, counter_street, counter_number,
 counter_postalCode, counter_city, series, aa, issueDate, invoiceType,
 vatPaymentSuspension, currency, exchangeRate, selfPricing, dispatchDate,
 dispatchTime, vehicleNumber, movePurspose, totalNetValue, totalVatAmount,
 totalWithheldAmount, totalFeesAmount, totalStampDutyamount, 
 totalOtherTaxesAmount, totalDeductionsAmount, 
 totalGrossValue, ComId, BraId, unid, stId, xmlResult, invoicePer,
 IncOrExp, SOrR, iFromEfar, paymentType, unidCaller, 
 correlatedInvoices, cancelledByMark 
 )
 AS (
 SELECT invId, uid, mark, counter_id, counter_vatNumber, counter_country,
 counter_branch, counter_name, counter_street, counter_number,
 counter_postalCode, counter_city, series, aa, issueDate, invoiceType,
 vatPaymentSuspension, currency, exchangeRate, selfPricing, dispatchDate,
 dispatchTime, vehicleNumber, movePurspose, totalNetValue, totalVatAmount,
 totalWithheldAmount, totalFeesAmount, totalStampDutyamount, 
 totalOtherTaxesAmount, totalDeductionsAmount, 
 totalGrossValue, ComId, BraId, unid, stId, xmlResult,
 (SELECT TtdtD_Desc 
 FROM DBCOMMON.dbo.TimTaxDocTypeD AS TTDT
 WHERE (TtdtD_Code = invoiceHeader.invoiceType)) AS invoicePer, IncOrExp,
 SOrR, iFromEfar, 
 (SELECT TOP 1 type FROM invoicePayments WHERE ((invoiceHeader.ComId = 1) OR (invoiceHeader.ComId IS NULL)) AND ((invoicePayments.ComId = 1) OR (invoicePayments.ComId IS NULL))
 AND (invoiceHeader.LgLRec = 1 AND invoiceHeader.LgLRec IS NOT NULL)
 AND (invoicePayments.LgLRec = 1 AND invoicePayments.LgLRec IS NOT NULL)
 AND invoicePayments.headid = invoiceHeader.unid 
 ORDER BY invoicePayments.unid) AS paymentType, unidCaller, 
 correlatedInvoices, cancelledByMark 
 FROM invoiceHeader WHERE ((invoiceHeader.ComId = 1) OR (invoiceHeader.ComId IS NULL))
 AND (invoiceHeader.LgLRec = 1 AND invoiceHeader.LgLRec IS NOT NULL)
 AND IncOrExp = 1
 AND invoiceHeader.issueDate BETWEEN '2021/01/01'
 AND '2021/12/31'
 AND invoiceHeader.stId = 0
 UNION ALL 
 SELECT invId, [uid], mark, counter_id, counter_vatNumber, counter_country,
 counter_branch, counter_name, counter_street, counter_number,
 counter_postalCode, counter_city, series, aa,  issueDate, invoiceType,
 vatPaymentSuspension,  currency,  exchangeRate, selfPricing,
 dispatchDate, dispatchTime, vehicleNumber, movePurspose,
 isnull([1] , 0) AS totalNetValue, isnull([2] , 0) AS totalVatAmount,
 isnull([3] , 0) AS totalWithheldAmount, 
 isnull([4] , 0) AS totalFeesAmount,
 isnull([5] , 0) AS totalStampDutyamount,
 isnull([6] , 0) AS totalOtherTaxesAmount,
 isnull([7] , 0) AS totalDeductionsAmount,
 isnull([1] , 0) + isnull([2] , 0) - isnull([3] , 0) + isnull([4] , 0) 
 + isnull([5] , 0) + isnull([6] , 0) - isnull([7] , 0) AS totalGrossValue,
 ComId , BraId, unid, stId, xmlResult, invoicePer, IncOrExp,
 SOrR, iFromEfar, paymentType, unidCaller, 
 correlatedInvoices, cancelledByMark 
 FROM 
 (
  SELECT 
  Glh_Id AS invId,  '' AS [uid], 0 AS mark, GelKinHeader.Glh_KvdPel AS counter_id,
 Pel_Afm AS counter_vatNumber, (SELECT CDescr FROM Xores
  INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS PXor ON Xores.Xor_Country = PXor.Id 
 WHERE Type = 200017 AND Xor_Id = PelMas.Pel_KvdXvra) AS counter_country, 
 GelKinHeader.BraId AS counter_branch, PelMas.Pel_Onoma AS counter_name,
 PelMas.Pel_Odos AS counter_street, PelMas.Pel_Arith AS counter_number,
 PelMas.Pel_TK AS counter_postalCode, (SELECT GPar_Per FROM GenParam 
 WHERE GPar_Typos = 'PERIOXES' AND GPar_Id = PelMas.Pel_Perioxh) 
 AS counter_city, GelKinHeader.Glh_Seira AS series, 
 CAST(GelKinHeader.Glh_ArParastatikou AS NVARCHAR(100)) AS aa, 
 GelKinHeader.Glh_DateKin AS issueDate, TtdtD_Code AS invoiceType,
  0 AS vatPaymentSuspension,  (SELECT CDescr FROM PelNomBasic 
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS PNom  
 ON PelNomBasic.PenB_currency = PNom.Id WHERE Type = 200018 
 AND PenB_Id = Glh_Nomisma) AS currency, Glh_Isotimia AS exchangeRate,
 GeaH_selfPricing AS selfPricing, null AS dispatchDate, 
 null AS dispatchTime, null AS vehicleNumber, 
 (SELECT GPar_movePurspose FROM GenParam WHERE GPar_Typos = 'SKOPOS'
  AND GPar_Id = Glh_IdSkopos) AS movePurspose, GLM_typeOfValue, 
 CASE GLD_PosoPis WHEN 0 THEN GLD_PosoXr ELSE GLD_PosoPis END AS Poso,
 GelKinHeader.ComId AS [ComId], GelKinHeader.BraId AS [BraId],
 0 AS [unid], -1 AS [stId], 0 AS [xmlResult], TtdtD_Desc AS invoicePer,
 1 AS [IncOrExp], GeaH_SendType AS SOrR, 2 AS iFromEfar,
 (SELECT Code FROM GenParam
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS TrPlhr 
 ON GenParam.GPar_paymentType = TrPlhr.Id
 WHERE GPar_Typos = 'TRPLHRVMHS'
 AND Type = 200019 AND GPar_Id = Glh_TrPlhr) AS paymentType, 
 0 AS unidCaller,
 Glh_correlatedInvoices AS correlatedInvoices, 
 Glh_cancelledByMark AS cancelledByMark
  FROM GelKinHeader INNER JOIN GelKinDetail ON GelKinDetail.GLD_ArAruroy = GelKinHeader.GLH_Aruro AND GelKinDetail.Gld_ProtAr = GelKinHeader.Glh_ProtAr
  INNER JOIN GelMas ON GelKinDetail.GKD_KvdLog = GelMas.Glm_Kvd
  INNER JOIN GelEtAruraHeader 
 ON GelKinHeader.Glh_ProtAr = GelEtAruraHeader.GeaH_Id
  INNER JOIN DBCOMMON.dbo.TimTaxDocTypeD AS TTDT  
 ON TTDT.TtdtD_Id = GelEtAruraHeader.GeaH_TaxDocTypeD
  LEFT OUTER JOIN PelMas ON GelKinHeader.Glh_KvdPel = PelMas.Pel_Id WHERE ((GelKinHeader.ComId = 1) OR (GelKinHeader.ComId IS NULL)) AND  ((GelEtAruraHeader.ComId = 1)  OR (GelEtAruraHeader.ComId IS NULL)) AND  ((GelMas.ComId = 1)  OR (GelMas.ComId IS NULL)) AND ((GelMas.Glm_Elp = 0) OR (GelMas.Glm_Elp IS NULL)) AND ((PelMas.ComId = 1) OR (PelMas.ComId IS NULL))
 AND GelKinHeader.Glh_KvdPel > 0 
 AND (GelKinHeader.Glh_Typos = 4)
 AND (GelKinHeader.Glh_TypeKin = 1)
 AND (GelEtAruraHeader.GeaH_SendType = 1)
 AND GelKinHeader.Glh_DateKin BETWEEN '2021/01/01'
 AND '2021/12/31'
 AND NOT EXISTS(SELECT unid FROM invoiceHeader  WHERE ((invoiceHeader.ComId = 1) OR (invoiceHeader.ComId IS NULL))
 AND (invoiceHeader.LgLRec = 1 AND invoiceHeader.LgLRec IS NOT NULL)
 AND IncOrExp = 1 
 AND invoiceHeader.iFromEfar = 2 
 AND invoiceHeader.invId = GelKinHeader.Glh_Id) 
 UNION ALL 
 SELECT  Glh_Id AS invId,  '' AS [uid], 0 AS mark,
 GelKinHeader.Glh_KvdPel AS counter_id, Kpb_Afm AS counter_vatNumber,
 (SELECT CDescr FROM Xores  INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS PXor
 ON Xores.Xor_Country = PXor.Id  WHERE Type = 200017 
 AND Xor_Id = KepPvlBasic.Kpb_KvdXvra) AS counter_country,
 GelKinHeader.BraId AS counter_branch, 
 KepPvlBasic.Kpb_Epvnymia AS counter_name,
 KepPvlBasic.Kpb_Address AS counter_street, 
 KepPvlBasic.Kpb_Arith AS counter_number, 
 KepPvlBasic.Kpb_Tk AS counter_postalCode, 
 (SELECT GPar_Per FROM GenParam  WHERE GPar_Typos = 'PERIOXES'
 AND GPar_Id = KepPvlBasic.Kpb_Perioxh)  AS counter_city, 
 GelKinHeader.Glh_Seira AS series,  
 CAST(GelKinHeader.Glh_ArParastatikou AS NVARCHAR(100)) AS aa, 
 GelKinHeader.Glh_DateKin AS issueDate, TtdtD_Code AS invoiceType,
 0 AS vatPaymentSuspension,
 (SELECT CDescr FROM PelNomBasic  INNER JOIN DBCOMMON.dbo.DBTAXPARAM 
 AS PNom   ON PelNomBasic.PenB_currency = PNom.Id WHERE Type = 200018  
 AND PenB_Id = Glh_Nomisma) AS currency, Glh_Isotimia AS exchangeRate,
 GeaH_selfPricing AS selfPricing, null AS dispatchDate,  
 null AS dispatchTime, null AS vehicleNumber,  
 (SELECT GPar_movePurspose FROM GenParam WHERE GPar_Typos = 'SKOPOS'  
 AND GPar_Id = Glh_IdSkopos) AS movePurspose,
 GLM_typeOfValue,  
 CASE GLD_PosoPis WHEN 0 THEN GLD_PosoXr ELSE GLD_PosoPis END AS Poso,
 GelKinHeader.ComId AS [ComId], 
 GelKinHeader.BraId AS [BraId], 0 AS [unid], -1 AS [stId], 
 0 AS [xmlResult], TtdtD_Desc AS invoicePer, 1 AS [IncOrExp],
 GeaH_SendType AS SOrR, 2 AS iFromEfar,
 (SELECT Code FROM GenParam
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS TrPlhr 
 ON GenParam.GPar_paymentType = TrPlhr.Id
 WHERE GPar_Typos = 'TRPLHRVMHS'
 AND Type = 200019 AND GPar_Id = Glh_TrPlhr) AS paymentType, 
 0 AS unidCaller,
 Glh_correlatedInvoices AS correlatedInvoices, 
 Glh_cancelledByMark AS cancelledByMark
 FROM GelKinHeader INNER JOIN GelKinDetail
 ON GelKinDetail.GLD_ArAruroy = GelKinHeader.GLH_Aruro 
 AND GelKinDetail.Gld_ProtAr = GelKinHeader.Glh_ProtAr  
 INNER JOIN GelMas ON GelKinDetail.GKD_KvdLog = GelMas.Glm_Kvd  
 INNER JOIN GelEtAruraHeader 
 ON GelKinHeader.Glh_ProtAr = GelEtAruraHeader.GeaH_Id  
 INNER JOIN DBCOMMON.dbo.TimTaxDocTypeD AS TTDT   
 ON TTDT.TtdtD_Id = GelEtAruraHeader.GeaH_TaxDocTypeD  
 INNER JOIN KepPvlBasic
 ON GelKinHeader.Glh_Afm = KepPvlBasic.Kpb_Afm WHERE ((GelKinHeader.ComId = 1) OR (GelKinHeader.ComId IS NULL)) AND  ((GelEtAruraHeader.ComId = 1)  OR (GelEtAruraHeader.ComId IS NULL)) AND  ((GelMas.ComId = 1)  OR (GelMas.ComId IS NULL)) AND ((GelMas.Glm_Elp = 0) OR (GelMas.Glm_Elp IS NULL)) AND ((KepPvlBasic.ComId = 1) OR (KepPvlBasic.ComId IS NULL))
 AND GelKinHeader.Glh_KvdPel = 0 
 AND GelKinHeader.Glh_Typos = 2 
 AND GelKinHeader.Glh_Afm <> '' AND GelKinHeader.Glh_Afm IS NOT NULL
 AND Glh_TypeKin = 1
 AND (GelEtAruraHeader.GeaH_SendType = 1)
 AND GelKinHeader.Glh_DateKin BETWEEN '2021/01/01'
 AND '2021/12/31'
 AND NOT EXISTS(SELECT unid FROM invoiceHeader  WHERE ((invoiceHeader.ComId = 1) OR (invoiceHeader.ComId IS NULL))
 AND (invoiceHeader.LgLRec = 1 AND invoiceHeader.LgLRec IS NOT NULL)
 AND IncOrExp = 1
 AND invoiceHeader.iFromEfar = 2 
 AND invoiceHeader.invId = GelKinHeader.Glh_Id) 
 ) AS SourceTable
 Pivot
 (
 SUM (Poso)
 FOR GLM_typeOfValue IN ([1], [2], [3], [4], [5], [6], [7])
 ) AS pivotTable 
 UNION ALL 
 SELECT TimHeader.Tih_AAEggrafhs AS invId,  '' AS uid, 0 AS mark,
 TimHeader.Tih_KvdPelProm AS counter_id, Pel_Afm AS counter_vatNumber,
 (SELECT CDescr FROM Xores
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS PXor ON Xores.Xor_Country = PXor.Id
 WHERE Type = 200017 AND Xor_Id = Pel_KvdXvra) AS counter_country,
 TimHeader.BraId AS counter_branch, PelMas.Pel_Onoma AS counter_name,
 PelMas.Pel_Odos AS counter_street, PelMas.Pel_Arith AS counter_number,
 PelMas.Pel_TK AS counter_postalCode,
 (SELECT GPar_Per FROM GenParam WHERE GPar_Typos = 'PERIOXES' 
 AND GPar_Id = PelMas.Pel_Perioxh) AS counter_city,
 TimHeader.Tih_Seira AS series,
 CAST(TimHeader.Tih_ArParastatikou AS NVARCHAR(100)) AS aa, 
 TimHeader.Tih_Date AS issueDate, TtdtD_Code AS invoiceType, 
 0 AS vatPaymentSuspension, 
 (SELECT CDescr FROM PelNomBasic
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS PNom 
 ON PelNomBasic.PenB_currency = PNom.Id
 WHERE Type = 200018 AND PenB_Id = Tih_XN) AS currency,
 Tih_Isotimia AS exchangeRate, 0 AS selfPricing, Tih_Date AS dispatchDate,
 Tih_VraApostolhs AS dispatchTime, Tih_ArFortosevs AS vehicleNumber,
 (SELECT Code FROM GenParam
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS Skopos 
 ON GenParam.GPar_movePurspose = Skopos.Id
 WHERE GPar_Typos = 'SKOPOS'
 AND Type = 200014 AND GPar_Id = Tih_IdSkopos) AS movePurspose, 
 SUM(Tid_AxiaYpokFpa) AS [totalNetValue], 
 SUM(Tid_AxiaFpa) AS [totalVatAmount], 
 0 AS totalWithheldAmount, 0 AS totalFeesAmount, 0 AS totalStampDutyamount, 
 0 AS totalOtherTaxesAmount, 0 AS totalDeductionsAmount, 
 Tih_TelAxia AS totalGrossValue, 
 TimHeader.ComId AS [ComId], TimHeader.BraId AS [BraId],0 AS [unid],
 -1 AS [stId], 0 AS [xmlResult], TtdtD_Desc AS invoicePer,
 Tip_TypeKin AS [IncOrExp], Tip_SendType AS SOrR, 101 AS iFromEfar,
 (SELECT Code FROM GenParam
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS TrPlhr 
 ON GenParam.GPar_paymentType = TrPlhr.Id
 WHERE GPar_Typos = 'TRPLHRVMHS'
 AND Type = 200019 AND GPar_Id = Tih_TroposPlhrvmhs) AS paymentType, 
 0 AS unidCaller,
 Tih_correlatedInvoices AS correlatedInvoices, 
 Tih_cancelledByMark AS cancelledByMark
 FROM TimHeader 
 INNER JOIN TimParastatika ON TimParastatika.Tip_SId = TimHeader.Tih_SId 
 AND TimParastatika.Tip_Seira = TimHeader.Tih_Seira
 AND TimParastatika.Tip_ArEntypou = TimHeader.Tih_SeiraEidosEntypou 
 AND TimParastatika.Tip_ArParastatikou = TimHeader.Tih_EidosEntypou
 INNER JOIN DBCOMMON.dbo.TimTaxDocTypeD AS TTDT 
 ON TTDT.TtdtD_Id = TimParastatika.Tip_TaxDocTypeD
 INNER JOIN PelMas ON TimHeader.Tih_KvdPelProm = PelMas.Pel_Id
 INNER JOIN TimDetail ON TimHeader.Tih_AAEggrafhs= TimDetail.Tid_HeadId WHERE ((TimHeader.ComId = 1) OR (TimHeader.ComId IS NULL)) AND ((PelMas.ComId = 1) OR (PelMas.ComId IS NULL))
 AND (TimParastatika.Tip_SendType = 1)
 AND (TimParastatika.Tip_TypeKin = 1)
 AND TimHeader.Tih_Date BETWEEN '2021/01/01'
 AND '2021/12/31'
 AND NOT EXISTS(SELECT unid FROM invoiceHeader  WHERE ((invoiceHeader.ComId = 1) OR (invoiceHeader.ComId IS NULL))
 AND (invoiceHeader.LgLRec = 1 AND invoiceHeader.LgLRec IS NOT NULL)
 AND IncOrExp = 1
 AND invoiceHeader.iFromEfar = 101 
 AND invoiceHeader.invId = TimHeader.Tih_AAEggrafhs) 
 GROUP BY  TimHeader.Tih_AAEggrafhs,  TimHeader.Tih_KvdPelProm, Pel_Afm, 
 Pel_KvdXvra, TimHeader.BraId, PelMas.Pel_Onoma, PelMas.Pel_Odos, 
 PelMas.Pel_Arith, PelMas.Pel_TK, Pel_Perioxh, TimHeader.Tih_Seira, 
 TimHeader.Tih_ArParastatikou, TimHeader.Tih_Date, TtdtD_Code, 
 Tih_XN, Tih_Isotimia, Tih_VraApostolhs, Tih_ArFortosevs, 
 TimHeader.Tih_IdSkopos, Tih_TelAxia, TimHeader.ComId, TtdtD_Desc, 
 Tip_TypeKin, Tip_SendType, Tih_TroposPlhrvmhs, 
 Tih_correlatedInvoices, Tih_cancelledByMark 
 UNION ALL 
 SELECT TimHeaderEx.Tih_AA AS invId,  '' AS uid, 0 AS mark,
 TimHeaderEx.Tih_KvdPelProm AS counter_id, Pel_Afm AS counter_vatNumber,
 (SELECT CDescr FROM Xores
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS PXor ON Xores.Xor_Country = PXor.Id
 WHERE Type = 200017 AND Xor_Id = Pel_KvdXvra) AS counter_country,
 TimHeaderEx.BraId AS counter_branch, PelMas.Pel_Onoma AS counter_name,
 PelMas.Pel_Odos AS counter_street, PelMas.Pel_Arith AS counter_number,
 PelMas.Pel_TK AS counter_postalCode,
 (SELECT GPar_Per FROM GenParam WHERE GPar_Typos = 'PERIOXES' 
 AND GPar_Id = PelMas.Pel_Perioxh) AS counter_city,
 TimHeaderEx.Tih_Seira AS series,
 CAST(TimHeaderEx.Tih_Arithmos AS NVARCHAR(100)) AS aa, 
 TimHeaderEx.Tih_DateKin AS issueDate, TtdtD_Code AS invoiceType, 
 0 AS vatPaymentSuspension, 
 (SELECT CDescr FROM PelNomBasic
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS PNom 
 ON PelNomBasic.PenB_currency = PNom.Id
 WHERE Type = 200018 AND PenB_Id = Tih_Nomisma) AS currency,
 Tih_Isotimia AS exchangeRate, 0 AS selfPricing, Tih_DateKin AS dispatchDate,
 Tih_VraApostolhs AS dispatchTime, Tih_ArFortosevs AS vehicleNumber,
 (SELECT Code FROM GenParam
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS Skopos 
 ON GenParam.GPar_movePurspose = Skopos.Id
 WHERE GPar_Typos = 'SKOPOS'
 AND Type = 200014 AND GPar_Id = Tih_IdSkopos) AS movePurspose, 
 SUM(Tid_AxiaYpokFpa) AS [totalNetValue], 
 SUM(Tid_AxiaFpa) AS [totalVatAmount], 
 0 AS totalWithheldAmount, 0 AS totalFeesAmount, 0 AS totalStampDutyamount, 
 0 AS totalOtherTaxesAmount, 0 AS totalDeductionsAmount, 
 Tih_TelikhAxia AS totalGrossValue, 
 TimHeaderEx.ComId AS [ComId], TimHeaderEx.BraId AS [BraId],0 AS [unid],
 -1 AS [stId], 0 AS [xmlResult], TtdtD_Desc AS invoicePer,
 Tip_TypeKin AS [IncOrExp], Tip_SendType AS SOrR, 102 AS iFromEfar,
 (SELECT Code FROM GenParam
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS TrPlhr 
 ON GenParam.GPar_paymentType = TrPlhr.Id
 WHERE GPar_Typos = 'TRPLHRVMHS'
 AND Type = 200019 AND GPar_Id = Tih_TroposPlhr) AS paymentType, 
 0 AS unidCaller,
 Tih_correlatedInvoices AS correlatedInvoices, 
 Tih_cancelledByMark AS cancelledByMark
 FROM TimHeaderEx 
 INNER JOIN TimParastEx 
 ON TimParastEx.Tip_ArParastatikou = TimHeaderEx.Tih_ArParastatikou 
 INNER JOIN DBCOMMON.dbo.TimTaxDocTypeD AS TTDT 
 ON TTDT.TtdtD_Id = TimParastEx.Tip_TaxDocTypeD
 INNER JOIN PelMas ON TimHeaderEx.Tih_KvdPelProm = PelMas.Pel_Id
 INNER JOIN TimDetailEx ON TimHeaderEx.Tih_AA = TimDetailEx.Tid_HeadId WHERE ((TimHeaderEx.ComId = 1) OR (TimHeaderEx.ComId IS NULL)) AND ((PelMas.ComId = 1) OR (PelMas.ComId IS NULL))
 AND (TimParastEx.Tip_SendType = 1)
 AND (TimParastEx.Tip_TypeKin = 1)
 AND TimHeaderEx.Tih_DateKin BETWEEN '2021/01/01'
 AND '2021/12/31'
 AND NOT EXISTS(SELECT unid FROM invoiceHeader  WHERE ((invoiceHeader.ComId = 1) OR (invoiceHeader.ComId IS NULL))
 AND (invoiceHeader.LgLRec = 1 AND invoiceHeader.LgLRec IS NOT NULL)
 AND IncOrExp = 1 
 AND invoiceHeader.iFromEfar = 102 
 AND invoiceHeader.invId = TimHeaderEx.Tih_AA) 
 GROUP BY  TimHeaderEx.Tih_AA,  TimHeaderEx.Tih_KvdPelProm, Pel_Afm, 
 Pel_KvdXvra, TimHeaderEx.BraId, PelMas.Pel_Onoma, PelMas.Pel_Odos, 
 PelMas.Pel_Arith, PelMas.Pel_TK, Pel_Perioxh, TimHeaderEx.Tih_Seira, 
 TimHeaderEx.Tih_Arithmos, TimHeaderEx.Tih_DateKin, TtdtD_Code, 
 Tih_Nomisma, Tih_Isotimia, Tih_VraApostolhs, Tih_ArFortosevs, 
 TimHeaderEx.Tih_IdSkopos, Tih_TelikhAxia, TimHeaderEx.ComId, TtdtD_Desc, 
 Tip_TypeKin, Tip_SendType, Tih_TroposPlhr, 
 Tih_correlatedInvoices, Tih_cancelledByMark 
 )
 SELECT ROW_NUMBER() OVER(ORDER BY invId ASC) AS [a/a], 0 AS [select],
 uid, mark, invId, counter_id, counter_vatNumber, counter_country, 
 counter_branch, counter_name, counter_street, counter_number, 
 counter_postalCode, counter_city, series, aa, issueDate, invoiceType, 
 vatPaymentSuspension, currency, exchangeRate, selfPricing, dispatchDate, 
 dispatchTime, vehicleNumber, movePurspose, totalNetValue, totalVatAmount, 
 totalWithheldAmount, totalFeesAmount, totalStampDutyamount, 
 totalOtherTaxesAmount, totalDeductionsAmount, 
 totalGrossValue, ComId, BraId, unid, null AS [status], stId, xmlResult,
 invoicePer, [IncOrExp], SOrR, iFromEfar, paymentType, unidCaller, 
 correlatedInvoices, cancelledByMark 
 FROM cte

then for every row of this query, I make the second query:

;with cte (invId, lineNumber, measurementUnit, invoiceDetailType, netValue,
 vatCategory, vatAmount, vatExemptionCategory, discountOption,
 withheldAmount, withheldPercentCategory, stampDutyAmount,
 stampDutyPercentCategory, feesAmount, feesPercentCategory,
 otherTaxesPercentCategory, otherTaxesAmount, deductionsAmount,
 lineComments, ComId, BraId, recType, taxCategory,
 classificationType, classificationCategory, classificationVat
 )
 AS (
 SELECT invoiceDetails.invId, lineNumber, measurementUnit,
 invoiceDetailType, netValue, 
 vatCategory, vatAmount, vatExemptionCategory, discountOption, 
 withheldAmount, withheldPercentCategory, stampDutyAmount, 
 stampDutyPercentCategory, feesAmount, feesPercentCategory, 
 otherTaxesPercentCategory, otherTaxesAmount, deductionsAmount, 
 lineComments, invoiceHeader.ComId , invoiceHeader.BraId,
 invoiceDetails.recType, invoiceDetails.taxCategory, 
 CASE DBTAXPARAM.isVat WHEN 1 THEN '' 
 ELSE invClassificationType.classificationType 
 END AS classificationType,
 classificationCategory,
 CASE DBTAXPARAM.isVat WHEN 1 THEN 
 invClassificationType.classificationType ELSE '' 
 END AS classificationVat
 
 FROM invoiceDetails
 INNER JOIN invoiceHeader
 ON invoiceHeader.unid = invoiceDetails.headid
 INNER JOIN invClassificationType 
 ON invoiceHeader.unid = invClassificationType.headid
 AND invoiceDetails.unid = invClassificationType.headidD
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS DBTAXPARAM 
 ON DBTAXPARAM.Code = invClassificationType.classificationType WHERE ((invoiceHeader.ComId = 1) OR (invoiceHeader.ComId IS NULL)) AND ((invoiceDetails.ComId = 1) OR (invoiceDetails.ComId IS NULL))
 AND (invoiceHeader.LgLRec = 1 AND invoiceHeader.LgLRec IS NOT NULL)
 AND (invoiceDetails.LgLRec = 1 AND invoiceDetails.LgLRec IS NOT NULL)
 AND invoiceHeader.invId = 3
 UNION ALL 
 SELECT Tih_AAEggrafhs AS invId, 0 AS lineNumber,
 ISNULL(invoiceDetailTypeCode.Code, 0) AS invoiceDetailType,
 0 AS invoiceDetailType, 
 SUM(Tid_AxiaYpokFpa) AS netValue, 
 (SELECT PFpa.Code
 FROM TrnKvdFpa 
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS PFpa 
 ON TrnKvdFpa.Kvd_vatCategory = PFpa.Id
 WHERE (PFpa.Type = 200003) 
 AND (TimDetail.Tid_KvdFpa = TrnKvdFpa.Kvd_Poso)) AS vatCategory,
 SUM(Tid_AxiaFpa) AS vatAmount,
 ISNULL(vatExemptionCode.Code, 0) AS vatExemptionCategory,
 0 AS discountOption, 0 AS withheldAmount, 
 CASE recTypeCode.Code WHEN 1 THEN ISNULL(taxesCode.Code, 0)
 ELSE (SELECT DBCOMMON.dbo.DBTAXPARAM.Code
 FROM DBCOMMON.dbo.DBTAXPARAM
 WHERE taxesCode.Code = DBCOMMON.dbo.DBTAXPARAM.id
 AND [Type] = 200005)
 END AS withheldPercentCategory,
 0 AS stampDutyAmount,
 CASE recTypeCode.Code WHEN 4 THEN ISNULL(taxesCode.Code, 0)
 ELSE (SELECT DBCOMMON.dbo.DBTAXPARAM.Code
 FROM DBCOMMON.dbo.DBTAXPARAM
 WHERE taxesCode.Code = DBCOMMON.dbo.DBTAXPARAM.id
 AND [Type] = 200007)
 END AS stampDutyPercentCategory,
 0 AS feesAmount, 
 CASE recTypeCode.Code WHEN 2 THEN ISNULL(taxesCode.Code, 0)
 ELSE (SELECT DBCOMMON.dbo.DBTAXPARAM.Code
 FROM DBCOMMON.dbo.DBTAXPARAM
 WHERE taxesCode.Code = DBCOMMON.dbo.DBTAXPARAM.id
 AND [Type] = 200008)
 END AS feesPercentCategory,
 CASE recTypeCode.Code WHEN 3 THEN ISNULL(taxesCode.Code, 0)
 ELSE (SELECT DBCOMMON.dbo.DBTAXPARAM.Code
 FROM DBCOMMON.dbo.DBTAXPARAM
 WHERE taxesCode.Code = DBCOMMON.dbo.DBTAXPARAM.id
 AND [Type] = 200006)
 END AS otherTaxesPercentCategory,
 0 AS otherTaxesAmount, 
 0 AS deductionsAmount, '' AS lineComments, TimHeader.ComId AS [ComId], 
 TimHeader.BraId AS [BraId],
 ISNULL(recTypeCode.Code, 0) AS recType,
 ISNULL(taxesCode.Code, 0) As taxCategory,
 ISNULL(classificationType.Code, 0) As classificationType,
 ISNULL(classificationCategory.Code, 0) As classificationCategory,
 ISNULL(classificationVat.Code, 0) As classificationVat
 FROM TimHeader 
 INNER JOIN TimParastatika ON TimParastatika.Tip_SId = TimHeader.Tih_SId 
 AND TimParastatika.Tip_Seira = TimHeader.Tih_Seira
 AND TimParastatika.Tip_ArEntypou = TimHeader.Tih_SeiraEidosEntypou 
 AND TimParastatika.Tip_ArParastatikou = TimHeader.Tih_EidosEntypou
 INNER JOIN DBCOMMON.dbo.TimTaxDocTypeD AS TTDT 
 ON TTDT.TtdtD_Id = TimParastatika.Tip_TaxDocTypeD
 INNER JOIN PelMas ON TimHeader.Tih_KvdPelProm = PelMas.Pel_Id
 INNER JOIN TimDetail ON TimHeader.Tih_AAEggrafhs= TimDetail.Tid_HeadId
 INNER JOIN ApoMas ON TimDetail.Tid_KvdEidous = ApoMas.Map_Kvdik
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS recTypeCode
 ON recTypeCode.Id = ApoMas.Map_recType
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS taxesCode
 ON taxesCode.Id = ApoMas.Map_taxCategory
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS vatExemptionCode
 ON vatExemptionCode.Id = PelMas.Pel_vatExemptionCategory
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS invoiceDetailTypeCode
 ON invoiceDetailTypeCode.Id = ApoMas.Map_invoiceDetailType
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS classificationCategory
 ON classificationCategory.Id = ApoMas.Map_classificationCategoryI
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS classificationType
 ON classificationType.Id = TimParastatika.Tip_classificationType
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS classificationVat
 ON classificationVat.Id = TimParastatika.Tip_classificationVat
 WHERE Tih_AAEggrafhs = 3
 AND NOT EXISTS(SELECT unid FROM invClassificationType  WHERE ((invClassificationType.ComId = 1) OR (invClassificationType.ComId IS NULL))
 AND (invClassificationType.LgLRec = 1 AND invClassificationType.LgLRec IS NOT NULL)
 AND invClassificationType.invId = TimHeader.Tih_AAEggrafhs)
 GROUP BY Tih_AAEggrafhs, Tid_KvdFpa, TimHeader.ComId, 
 TimHeader.BraId, 
 taxesCode.Code, recTypeCode.Code, vatExemptionCode.Code,
 classificationType.Code,
 classificationCategory.Code,
 classificationVat.Code,
 invoiceDetailTypeCode.Code  UNION ALL 
 SELECT TiEA_TimId AS invId, 0 AS lineNumber,
 0 measurementUnit,
 ISNULL(invoiceDetailTypeCode.Code, 0) AS invoiceDetailType,
 SUM(TiEA_Poso) AS netValue,
 (SELECT PFpa.Code
 FROM TrnKvdFpa
 INNER JOIN DBCOMMON.dbo.DBTAXPARAM AS PFpa
 ON TrnKvdFpa.Kvd_vatCategory = PFpa.Id
 WHERE (PFpa.Type = 200003)
 AND (TimXrevseis.Tix_PosostoFpa = TrnKvdFpa.Kvd_Poso)) AS vatCategory,
 SUM(TiEA_VatValue) AS vatAmount,
 ISNULL(vatExemptionCode.Code, 0) AS vatExemptionCategory,
 0 AS discountOption, 0 AS withheldAmount,
 CASE recTypeCode.Code WHEN 1 THEN ISNULL(taxesCode.Code, 0)
 ELSE (SELECT DBCOMMON.dbo.DBTAXPARAM.Code
 FROM DBCOMMON.dbo.DBTAXPARAM
 WHERE taxesCode.Code = DBCOMMON.dbo.DBTAXPARAM.id
 AND [Type] = 200005)
 END AS withheldPercentCategory,
 0 AS stampDutyAmount,
 CASE recTypeCode.Code WHEN 4 THEN ISNULL(taxesCode.Code, 0)
 ELSE (SELECT DBCOMMON.dbo.DBTAXPARAM.Code
 FROM DBCOMMON.dbo.DBTAXPARAM
 WHERE taxesCode.Code = DBCOMMON.dbo.DBTAXPARAM.id
 AND [Type] = 200007)
 END AS stampDutyPercentCategory,
 0 AS feesAmount,
 CASE recTypeCode.Code WHEN 2 THEN ISNULL(taxesCode.Code, 0)
 ELSE (SELECT DBCOMMON.dbo.DBTAXPARAM.Code
 FROM DBCOMMON.dbo.DBTAXPARAM
 WHERE taxesCode.Code = DBCOMMON.dbo.DBTAXPARAM.id
 AND [Type] = 200008)
 END AS feesPercentCategory,
 CASE recTypeCode.Code WHEN 3 THEN ISNULL(taxesCode.Code, 0)
 ELSE (SELECT DBCOMMON.dbo.DBTAXPARAM.Code
 FROM DBCOMMON.dbo.DBTAXPARAM
 WHERE taxesCode.Code = DBCOMMON.dbo.DBTAXPARAM.id
 AND [Type] = 200006)
 END AS otherTaxesPercentCategory,
 0 AS otherTaxesAmount,
 0 AS deductionsAmount, '' AS lineComments, TimHeader.ComId AS [ComId],
 TimHeader.BraId AS [BraId],
 ISNULL(recTypeCode.Code, 0) AS recType,
 ISNULL(taxesCode.Code, 0) As taxCategory,
 ISNULL(classificationType.Code, 0) As classificationType,
 ISNULL(classificationCategory.Code, 0) As classificationCategory,
 ISNULL(classificationVat.Code, 0) As classificationVat
 FROM TimHeader
 INNER JOIN TimParastatika ON TimParastatika.Tip_SId = TimHeader.Tih_SId
 AND TimParastatika.Tip_Seira = TimHeader.Tih_Seira
 AND TimParastatika.Tip_ArEntypou = TimHeader.Tih_SeiraEidosEntypou
 AND TimParastatika.Tip_ArParastatikou = TimHeader.Tih_EidosEntypou
 INNER JOIN DBCOMMON.dbo.TimTaxDocTypeD AS TTDT
 ON TTDT.TtdtD_Id = TimParastatika.Tip_TaxDocTypeD
 INNER JOIN PelMas ON TimHeader.Tih_KvdPelProm = PelMas.Pel_Id
 INNER JOIN TimDetail ON TimHeader.Tih_AAEggrafhs= TimDetail.Tid_HeadId
 INNER JOIN TimEA ON TimDetail.Tid_AAEggrafhs = TimEA.TiEA_TimDetId 
 AND TimDetail.Tid_subId = TimEA.TiEA_RowGrid 
 AND TimDetail.Tid_HeadId = TimEA.TiEA_TimId 
 INNER JOIN TimXrevseis ON TimEA.TiEA_IdExp = TimXrevseis.Tix_Id
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS recTypeCode
 ON recTypeCode.Id = TimXrevseis.Tix_recType
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS taxesCode
 ON taxesCode.Id = TimXrevseis.Tix_taxCategory
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS vatExemptionCode
 ON vatExemptionCode.Id = TimXrevseis.Tix_vatExemptionCategory
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS invoiceDetailTypeCode
 ON invoiceDetailTypeCode.Id = TimXrevseis.Tix_invoiceDetailType
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS classificationCategory
 ON classificationCategory.Id = TimXrevseis.Tix_classificationCategoryI
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS classificationType
 ON classificationType.Id = TimXrevseis.Tix_classificationTypeI
 LEFT OUTER JOIN (SELECT  Id, Code, Descr
 FROM DBCOMMON.dbo.DBTAXPARAM) AS classificationVat
 ON classificationVat.Id = TimXrevseis.Tix_classificationVat
 WHERE Tih_AAEggrafhs = 3
 AND (TiEA_Poso <> 0 OR TiEA_VatValue <> 0)
 AND (((TimXrevseis.Tix_typeOfValue = 1)  AND (TimXrevseis.Tix_typeOfValue <> 2) AND (TimXrevseis.Tix_typeOfValue IS NOT NULL ))
 OR ( (TimXrevseis.Tix_typeOfValue >= 1)  AND (Tix_recType > 0) AND (Tix_recType IS NOT NULL)))
 AND NOT EXISTS(SELECT unid FROM invClassificationType  WHERE ((invClassificationType.ComId = 1) OR (invClassificationType.ComId IS NULL))
 AND (invClassificationType.LgLRec = 1 AND invClassificationType.LgLRec IS NOT NULL)
 AND invClassificationType.invId = TimHeader.Tih_AAEggrafhs)
 GROUP BY TimEA.TiEA_TimId, Tix_PosostoFpa, TimHeader.ComId,
 TimHeader.BraId, vatExemptionCode.Code,
 Tix_typeOfValue, recTypeCode.Code, taxesCode.Code,
 classificationType.Code,
 classificationCategory.Code,
 classificationVat.Code,
 invoiceDetailTypeCode.Code 
 )
 SELECT
 invId,
 DENSE_RANK() OVER(PARTITION BY invId ORDER BY vatCategory ASC, recType ASC, invoiceDetailType ASC) AS lineNumber,
 measurementUnit, invoiceDetailType, SUM(netValue) AS netValue,
 vatCategory, SUM(vatAmount) AS vatAmount, vatExemptionCategory, discountOption,
 SUM(withheldAmount) AS withheldAmount, withheldPercentCategory,
 SUM(stampDutyAmount) AS stampDutyAmount, stampDutyPercentCategory,
 SUM(feesAmount) AS feesAmount, feesPercentCategory,
 otherTaxesPercentCategory, SUM(otherTaxesAmount) AS otherTaxesAmount,
 SUM(deductionsAmount) AS deductionsAmount,
 lineComments , ComId, BraId, recType, taxCategory, 
 classificationType,
 classificationCategory
, classificationVat
 FROM cte 
 WHERE lineNumber = 0
 GROUP BY invId, vatCategory, measurementUnit, invoiceDetailType, vatExemptionCategory,
 discountOption, withheldPercentCategory, stampDutyPercentCategory, feesPercentCategory,
 otherTaxesPercentCategory, lineComments, ComId, BraId, recType, taxCategory,
 classificationType,
 classificationCategory
, classificationVat
 ORDER BY invId, lineNumber

and from this query I write in threetables:
invoiceHeader
invoiceDetail
invoiceClassification

and I make an other query for inserting in table invoicePayments and another to insert in invoiceTaxes.