Owner Acceptance of Nonconforming Work

Hi! 

A201, Article 12.3: Acceptance of Nonconforming Work

"If the owner prefers to accept work that is not in accordance with the requirements of the contract documents, the owner may do so instead of requiring its removal and correction, in which case the contract sum will be reduced as appropriate and equitable. Such adjustment shall be effected whether or not final payment has been made." 

If final payment has been made, what is the procedure for this? That is, can a change order still be prepared?