No, arrears are not cleared by such a negotiation. Only the court can do something like that. Remember, child support BELONGS TO THE CHILD and cannot be negotiated away by the parents.
This is a rephrase of a question that you also posted. You need to bring your issues in fornt of the Magistrate or Judge who entered the original order. If there is a court order requiring you to signe the waiver for even years, it is best not to violate the order. If he was supposed to have the kids half the time and is not, you need a modification entered. Good luck.