The issue of the defects certificate is not dependent upon the final payment certificate. Instead it depends upon the defects date set out in the contract data part one of your subcontract. This will usually be defined as being a stated number of weeks after the date when the whole of your subcontract works achieved completion (defined in clause 11.2(2)). But the contractor may have changed that, for example by tying your defects date into the defects date of the main contract it has with the employer. So, your first task must be to examine your subcontract to see what the defects date is defined as.
A defect can only be notified to you by the contractor up until the defects date, see clause 42.2. If, as it seems, the defects date has long since passed, the defects certificate should have been issue to you by the contractor at the defects date, see clause 42.2.
Your final remedy is to use the adjudication procedure in option W2 to require the defects certificate to be issued and any outstanding retention released, see the last part of clause X16.2.