The loop

while (<$a_fh>) {
    print unless exists $second_file{unpack 'A*', $_};
}
[download]

eats up the whole file. Maybe your intention was like:

while (<$file_a>) {
    unless (exists $h{unpack 'A*', $_}) {
        print;
    } else {
        last;
    }
}
[download]

And then there is of course the other issue with using <$file_x> in list context as already described by Fletch and the questionable use of unpack.

-jo