check if the last but one letter from the first digit is always a "Y"

Assuming you mean "last but one letter after the first digit", this seems to work:

$re = qr[\d+\D+Y\D(\d|$)];;

print '\\files\builds\data\M9998SBQCACSYD30401S' =~ $re ? 'yes' : 'no'
+;;
yes

print '\\files\builds\data\M9998SBQCACSXD30401S' =~ $re ? 'yes' : 'no'
+;;
no
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The regex says:

$re = qr[
    \d+    # after the first (and any subsequent digits )
    \D*    # there should be some none digits
    Y      # and a Y
    \D     # followed by only one more non-digit
    (\d|$) # before another digit or end of string
]x;
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