What are the legal basis for constructive waivers according to the common law? How we will be able to define / support the owner's position?

Any constructional project has effective and completion date, and during the performance process of the project there is a period for commissioning services. My Q is if a company paid for the commissioning services already, later-on and #1 before the commissioning begin, the owner “company” requested a change order on the project, therefore the commissioning sevs. stopped and contractor begin working on the change order. After all, #2 contractor have been paid for the change and commissioning sevs. of that change, and everything till this point was satisfied. #3 Four years later, the owner came back to contractor and asked him to return its money back for #1 the commissioning sevs. that was paid prior the change order and before the commissioning services take place, however contractor refused to returning the money back claiming that the owner waived his right for the payment because he spent 4 years without providing notice. ((Refer to the Federal Acquisition Regulations, please)