Reduce your problem as much as you can, e.g.

$ echo -e "old\nfarts\nsmell"  > foo
$ cat foo
old
farts
smell
$ perl
use strict;
use warnings;
my $fh = undef;
open ($fh, "<", 'foo') or die "Can't open: $!";
while (<$fh>) {
    chomp;
    $fh =~ s/old/new/g;
}
close ($fh) or die "Can't close: $!";
__END__
$ cat foo
old
farts
smell
[download]

The file was not updated, which means your use of the replace operator on the filehandle probably doesn't work as you expect.

Also, consider using the readmore tags since your code is extensive. See Perl Monks Approved HTML tags.