Do you mean charge for the physical after you've billed it with the diagnos pertaining to the knee problem, and that was applied to deductible?
If that is the case, I'm thinking NO unless the documentation supports it but then you would need to file a corrected claim, but I'm still thinking it's going to go towards deductible. If it's a group health plan you could "try" an appeal but you should attach the providers notes for that visit to see if it qualifies but you'll want a copy of the patient's plan SPD as they may be grandfathered and not contain the physicial exam benefit with no OOP.
As for waiving the oop, that definetely would not be adviseable unless the patient falls into your financial hardship qualifications as per your office financial policy. If it doesn't you could waive it but it would be moot because you'll legally need to file a corrected claim showing the reduction in fee to the carrier.