Am I correct in understanding that you have a Perl script that is acting to modify a file that happens to contain text that is (or at least looks like) a Perl script?

The s/// operator is not the system() function. This remains true notwithstanding the fact that the text that it happens be acting on looks like a line of Perl code with a system() function in it.

The sequence \p in a Perl regular expression has a meaning (to do with Unicode).