The provisions are contained within Option Y(UK)2, under clause Y2.3.
This clause should state when a ‘Pay Less’ notice is to be notified to ensure that it is enforceable, which is either the ‘prescribed period’, as stated in the Scheme for Construction Contracts, or as agreed by the parties (and stated in Y2.3).
Re-reading your question, the certificate and any ‘Pay Less’ notice are separate procedures.
A ‘Pay Less’ notice effectively applies to a situation where an Employer wishes to ‘set off’ monies against an amount certified.
Where a certificate is less than the amount applied, the basis on which the sum is calculated must be provided to be compliant but this does not require a ‘Pay Less’ notice.