Always start your scripts with

use strict;
use warnings;
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It catches many of your errors. The correct comparison is either $byte eq "\x00" or $byte eq chr(0x00).

You can still use a substitution if your mapping is constant:

my %table = (
   "\x00" => "\x17",
   "\x17" => "\x00",
   ...
);
my $re = join '|', map quotemeta, keys %table;

# open in and out files...
# and then substitute:

$str =~ s/($re)/$table{$1}/g
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