The normal payment timescales - i.e. the assessment interval - and mechanisms continue on after the Completion Date. So if you make an application and claim the full amount, the the PM will, in his assessment, have to give reasons for deducting those amounts.
If you disagree with those amounts, a dispute has crystallised, so you could go to Adjudication, which I would only advise doing so after trying to escalate it to the PM and then the Employer.
A more fruitful avenue might be this : you are entitled to interest on the amounts from when they became due provided you applied for them i.e. a mistake by the PM (see clause 51.3) , so you could include in your application interest on these outstanding amounts from the time that you starting applying for them. That - along with a word to the PM - might nudge the QS in the direction you want.