Removing specific string in autoexec.bat

I am trying to find a way to remotely edit approximately 5000 Win9X machines. What I need to do is REMARK (REM out) one particular string that could be located anywhere in the autoexec.bat. Does anyone have any idea of how this can be done? Java script or any other type of script? Or better yet has anyone done it? I really don’t want to have to visit all these machines or do individual remote sessions for each machine.