You output to a third file. Let's fix that.

my $file_a = '...';
my $file_b = '...';

my %lines;

{
   open my $fh, '<', $file_a
      or die "Can't open index file \"$file_a\": $!\n";

   while (<$fh>) {
      $lines{$.} = 1 if /X/;
   }
}

{
   # Immitate "perl -pi".
   local $^I   = '';
   local @ARGV = $file_b;

   my $count = 0;
   while (<>) {
      s/(Y)/ exists $lines{ ++$count } ? 'Z' : $1 /eg;
      print;
   }
}
[download]

Also fixed:

• Used lexical variables instead of package variable whenever possible.
• Removed the source line number from error messages likely caused by user error. By adding a descriptive name for the file in the error message — I used "index" since I'm not sure what the file is — the error message is easily locatable without the line number.

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