In etwa so:
[autoit]#include <File.au3>
$Pfad = "C:\Test" ;Abschließender Backslash ist wichtig!!!
$FileList = _FileListToArray($Pfad, "*.properties", 1)
$hFile = FileOpen("Debug.txt", 1)
For $i = 1 To UBound($FileList) - 1
$k = $FileList[$i]
Run("C:\Programme\Java\jdk1.7.0_45\bin\native2ascii -reverse -encoding utf8 " & $Pfad & $k & " " & $Pfad & $k, @SW_HIDE, $STDERR_CHILD + $STDOUT_CHILD)
Do
FileWriteLine($hFile, StdOutRead($hProgram))
Until Not ProcessExists($hProgram)
Next
FileClose($hFile)