Your payment obligations continue to apply in the ECC right up until four weeks after the supervisor has issued the defects certificate – see clause 50.1. That means that your project manager should be issuing certificates for payment throughout that period, even if they are zero valued.
The contractor is paid the amount due – see clauses 50.2, 51.1 and 51.2. If the amount due reduces, presumably because of some wrongly assessed amount, the project manager can and should correct the amount due – see clause 50.5. If that reduces the amount due then the third sentence of clause 51.1 requires the contractor to make a payment for the difference to the employer. Therefore, in answer to your question, you are able to retrieve this overpayment from the contractor.
In addition, the contractor is required to pay interest on the amount he has been overpaid, in exactly the same way as you are required to pay such interest on any underpayment – see clause 51.3.
What should happen is that your project manager makes an assessment based upon the agreed amount and issues a certificate requiring the contractor to pay the difference to you under clause 51.1. The contractor then pays you the certified amount in accordance with the timescales set out in clause 51.2. If the contractor is late in paying, then interest will accrue on that payment, again see clause 51.2.