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You have 2 places in your code where you have ) character that is not escaped and not quoted, so it is ending your code block prematurely.

You just need to escape the ) characters.

Thanks a lot! That solved my problem

REM Changes the permission of specified file to specified Access for specified group and logs the output. echo ------------ >> %Output% echo ***Change*** >> %Output% echo ------------ >> %Output% for /f "delims=" %%y in (%Input%) do ( echo icacls %%y /grant:r %Group%:(%Permission%) >> %Ou...