open A, '<', 'fileA' or die "Cannot open 'fileA' $!";

my %lines;
while ( <A> ) {
    $lines{ $. } = () if /X/;
    }

close A;

open B, '<', 'fileB' or die "Cannot open 'fileB' $!";

my $count;
while ( <B> ) {
    s/(Y)/ exists $lines{ ++$count } ? 'Z' : $1 /eg;
    print; # updated to print lines
    }

close B;