Ideally, you'd provide a list of more than 2 strings, but your description helps. The following will probably suit your needs:

my @list = (
    # Good
    "\\\\files\\builds\\data\\M9998SBQCACSYD30401S",
    # Bad
    "\\\\files\\builds\\data\\M9998SBQCACSAD30401S",
);

for my $x (@list) {
    if ($x =~ /Y[A-Z]\d[^\\]*$/){
        print "$x - matches\n";
    } else {
        print "$x - doesn't match\n";
    }
}
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Given that these are file paths, I personally would rely on File::Basename or File::Spec to separate the filenames from the directories before doing the tests. That way the code would still work on other platforms.