Sorry I did not read your first post carefully enough. This version should check all the lines where the first part matches and then write the lines to new file if anything else on the lines from file1 and file2 are different.
#include <file.au3>
Global $aArray1 = 0
Global $aArray2 = 0
Global $hDiff = -1
_FileReadToArray("C:File1.txt",$aArray1)
_FileReadToArray("C:File2.txt",$aArray2)
$hDiff = Fileopen("C:Diff.txt",10)
For $i = 1 To UBound($aArray1) - 1
$sID1 = StringLeft($aArray1[$i],StringInStr($aArray1[$i],"ý",1,1)-1)
For $j = 1 To UBound($aArray2) - 1
$sID2 = StringLeft($aArray2[$j],StringInStr($aArray2[$j],"ý",1,1)-1)
if $sID1 == $sID2 Then ;Check if the first part is the same
;then check if anything else on the lines is different
if $aArray1[$i] <> $aArray2[$j] Then
FileWriteLine($hDiff, "File1: Line" & $i & ":" & $aArray1[$i] & @CRLF & "File2: Line" & $j & ":" & $aArray2[$j])
endif
EndIf
next
Next
FileClose($hDiff)