You certainly should be able to change the file from within Perl. There is no reason to resort to an external program. Why is your script failing? What error messages does it report?

CGI scripts run as the user of the web server. On IIS, this is IUSR_machine. You need to check that the web user has permissions to write to the file you want to change. Otherwise, nothing will be able to change the file when spawned by the web server.