Unfortunately, a HDHP under Medicare is not HSA qualified.

You would remove the overage, once you do the math for what is his limit for the year, and do so before the due date (which includes extension) of that return. Make sure to remove any earnings, as well. Don't leave it and keep paying the 6% excise tax and it seems you won't have any amount to "let it ride, pay the fee once, then apply it to the next year" if he now is on Medicare.