$x should match the pattern Y(digit)(number)

Surely you mean Y(letter)(number)?

Try this:

$x =~ /Y[A-Z]\d+[^\d\\]*$/
[download]

as in

for  my $x ("\\\\files\\builds\\data\\M9998SBQCACSYD30401S", "\\\\file
+s\\builds\\data\\M9998SBQCACSAD30401S") {
    if($x =~ /Y[A-Z]\d+[^\d\\]*$/) {
        print "$x matches\n";
    } else {
        print "$x doesn't match\n";
    }
}
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which yields:

\\files\builds\data\M9998SBQCACSYD30401S matches
\\files\builds\data\M9998SBQCACSAD30401S doesn't match
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([^\d\\] makes sure you matched the last number, and no backslash follows.)