I think Forsaken is on the right track (your program is waiting for $/, which is now "\x00", to finish reading the user's input, but it is getting newlines instead), but I also think that you need that $/ = "\x00" for what your program is doing. Refraining from refactoring your code too much:

my $orig_IRS = $/;    # save the original input record separator
$/ = "\x00";

while (<$ORIG>) {

  $count = (($change = $_)
         =~ s/(\x33\x33\x39\x39.*?\x00)/"\x00" x length($1)/e);

  if ($count == null) {
    print $MOD $_;

  } else {

    local $/ = $orig_IRS;  # restore input record separator locally

    $answer = &promptUser("Modify $1?");
    if ($answer == "y") {
      print $MOD $change;
    } else {
      print $MOD $_;
    }
  }
[download]

Alternatively, you could set the terminal to raw mode, so that the user did not need to hit Enter after y/n. See the ReadMode function of Term::ReadKey.

Update: Another possibility is to make this single change to your script:

while ( defined ( $_ = do { local $/ = "\x00"; <$ORIG> } ) ) {
  # ...
}
[download]