It's not working because you lost the -i switch, which specifies edit-in-place. Do "perl --help" to get a list of command line switches. You really shouldn't invoke an external process, though, if you don't have to do so. Just follow the other idiom I mentioned. To elaborate...

open(OLD, "<old.txt") or die "can't open original file: $!";
open(NEW, ">new.txt") or die "can't open new file: $!";

while(<OLD>) {
    s/whatever/somethingelse/;
    print NEW;
}

close(OLD);
close(NEW)

rename("new.txt", "old.txt");
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