#Variables for Site URL and Library Name

$WebURL="Site URL"

$LibraryName="LIBRARYNAME"

#Get Site and Library

$Web = Get-SPWeb $WebURL

$DocLib = $Web.Lists.TryGetList($LibraryName)

#Get all Checked out files

$CheckedOutFiles = $DocLib.Items | Where-Object { $_.File.CheckOutStatus -ne "None"}

#Check in All Checked out Files in the library

ForEach($item in $CheckedOutFiles)

{

#If you want to update fields

    #$item["Field"] = "value"

    #$item.SystemUpdate()

    #check in file programmatically    

    #$item.TakeoverCheckout()

    $DocLib.GetItemById($item.Id).file.CheckIn("Checked in by Admin")

    write-host "File:'$($item.Name)' has been checked in!"      

}