Loop, Files, %A_Desktop%\*.*, DF
   files .= (A_Index = 1 ? "" : "|") . A_LoopFileName

Gui, Add, ListBox, w300 h200 vList1, % files
Gui, Add, Button, gCopy, Copy Selected
Gui, Show
Return

Copy:
   GuiControlGet, List1
   MsgBox, % List1
   Return

#NoEnv 
#SingleInstance force 
#Persistent   

nameBUT := StrSplit("SALES|Cashing|Button3|Button4|Button5|Button6|DocFiles|PdfFiles", "|")   

Gui Add, ListBox, w650 r10 vfiles1, % "Dir1 = " dir1 "| |" list1
Gui Add, ListBox, xm w650 r10 vfiles2, % "Dir2 = " dir2 "| |" list2
Gui Add, Button, w75 gGuiOK default, Exit
Gui,Add, Text, yp+5 x100,Dir1
Gui,Add, Edit, yp-3 x130 w200 vDir1,%dir1%
Gui,Add, Text, yp+2 x340,Dir2
Gui,Add, Edit, yp-3 x365 w200 vDir2,%dir2%
Gui,Add, Text, yp+2 x575,Mask
Gui,Add, Edit, yp-3 x605 w75 vFileMask,%fileMask%
Gui Add, Button, yp x685 w75 gGo, Go
Gosub, AddRightSideButtons
Gui Show, w775
Return

AddRightSideButtons:
    GuiControlGet, ctl, Pos, files1

    x := ctlX + ctlW + 10
    Gui, Add, Button, x%x% y%ctlY% w90 h28 gBUT, % nameBUT[1]  
    Loop, 7
        Gui, Add, Button, wp hp gBUT, % nameBUT[A_index+1]  
return

Go: 
    Gui, Submit, NoHide 
    gosub, DoTheWork
    GuiControl,,files1,% "|Dir1 = " dir1 "| |" list1
    GuiControl,,files2,% "|Dir2 = " dir2 "| |" list2
return

BUT:
If (A_GuiControl=nameBUT[1]){
    ControlSetText, Edit1, % "E:\ask\work"
    ControlSetText, Edit2, % "E:\ask\backup"
    }
Else
  If (A_GuiControl=nameBUT[2]){
      ControlSetText, Edit1,% "E:\ask\sales"
      ControlSetText, Edit2, % "E:\ask\work"
  }
Else
  If (A_GuiControl=nameBUT[7]){
      ControlSetText, Edit3, *.docx
      ControlClick, Go, Comp 
  }
Else
  If (A_GuiControl=nameBUT[8]){
      ControlSetText, Edit3, *.pdf
      ControlClick, Go, Go 
  }  
Else
    Msgbox % "NONE!!" A_GuiControl

return

GuiOK:
GuiClose:
GuiEscape:
ExitApp



DoTheWork:
filelist1 := filelist2 := ""
list1 := list2 := ""
fnb1 := fnb2 := 0 ; <<<<< added: initialize the counters
Loop %dir1%\%fileMask%
{
If ( A_LoopFileName ~= "~\$")
        continue
    fileList1 .= A_LoopFileName . "`n"
    fnb1++ ; <<<<< changed: don't use A_Index because some files may be skipped
}
StringTrimRight fileList1, fileList1, 1
Loop %dir2%\%fileMask%
{
    If ( A_LoopFileName ~= "~\$")
        continue
    fileList2 .= A_LoopFileName . "`n"
    fnb2++ ; <<<<< changed: don't use A_Index because some files may be skipped
}
StringTrimRight fileList2, fileList2, 1

If (fnb1 = 0) && (fnb2 = 0) ; <<<<< added: early return
    Return

Sort fileList1
Sort fileList2
StringSplit files_1_, fileList1, `n
StringSplit files_2_, fileList2, `n
idxF1 := idxF2 := 1

Loop
{
    If (idxF1 > fnb1) ; <<<<< moved to the top of the loop
    {
        Loop % fnb2 - idxF2 + 1
        {
            list1 .= " |"   ; Empty
            list2 .= files_2_%idxF2% . "|"
            idxF2++
        }
        Break
    }
    If (idxF2 > fnb2) ; <<<<< moved to the top of the loop
    {
        Loop % fnb1 - idxF1 + 1
        {
            list1 .= files_1_%idxF1% . "|"
            idxF1++
            list2 .= " |"   ; Empty
        }
        Break
    }
    If (files_1_%idxF1% = files_2_%idxF2%)
    {
        ; We are in synch
        list1 .= files_1_%idxF1% . "|"
        idxF1++
        list2 .= files_2_%idxF2% . "|"
        idxF2++
    }
    Else
    {
        ; Either file at idxF1 or at idxF3 is missing, we must find which one
        If (files_1_%idxF1% > files_2_%idxF2%)
        {
            ; Missing in first list
            list1 .= " |"   ; Empty
            list2 .= files_2_%idxF2% . "|"
            idxF2++
        }
        Else
        {
            ; Missing in second list
            list1 .= files_1_%idxF1% . "|"
            idxF1++
            list2 .= " |"   ; Empty
        }
    }
}

StringTrimRight list1, list1, 1
StringTrimRight list2, list2, 1
Return

Loop, parse, List1
Loop, parse, List2