After some tinkering:

use strict;
use warnings;

my $original = &promptUser("Enter original filename");
my $modified = &promptUser("Enter modified filename");

open(my $ORIG, "$original") or die "could not open $original";
binmode($ORIG);

open(my $MOD, ">$modified") or die "could not open $modified";
binmode($MOD);

# commented out $/ = "\x00";

while (<$ORIG>)
  {
  my $count = ((my $change = $_) =~ s/(\x33\x33\x39\x39.*?\x00)/"\x00"
+ x length($1)/e);
  if ($count == 0)
    { print $MOD $_; }
  else
    {
    my $answer = &promptUser("Modify $1?");
    if ($answer eq "y") # <-- eq for test, == is for numerical compari
+sons
      { print $MOD $change; }
    else
      { print $MOD $_; }
    }
  }

close $MOD;
close $ORIG;

sub promptUser
  {
  my($promptString, $defaultValue) = @_;

  if ($defaultValue)
    { print $promptString, "[", $defaultValue, "]: "; }
  else
    { print $promptString, ": "; }

   $| = 1;               # force a flush after print
   my $line = <STDIN>;         # get the input from STDIN

   chomp($line);

   if ($defaultValue)
     { return $line ? $line : $defaultValue; } # return $line if it ha
+s a value
   else
     { return $line; }
  }
[download]

Turns out it was your $/ that caused it. Btw, is there supposed to be only 1 change in the entire file?

Oh, and please, in the future, for the sake of your own sanity as well as ours:
- use strict;
- use warnings;
- indent
- just like in english(or other languages), a space after a comma please
- (personal opinion) assign $_ to a named variable if you're going to use that value for more than the most basic of functions.