i figured it out. The issue was that when i created the $re variable, it was adding the slashes. by using just what was inside the slashes of the original string, i managed to get it to work

            if(index($_[0],"qr/") >= 0){ 
                $_[0] =~s/qr[\/](.*?)([^\\])[\/](i?)$/$1$2/s;
                print $fh Dumper($_[0]);
                if($3=='i'){
                    $_[0] = qr/$_[0]/i;
                }else{
                    $_[0] = qr/$_[0]/;
                }
                print $fh Dumper($_[0]);
            }
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