Vendor Repayment

We have over billed a vendor in our AR system, for which they have paid in full. Normally we would just give them a credit on their account and it would wash out just fine. However, this was for a specific project which has now completed and we are no longer doing business with this vendor so we would like to cut them a check from AP. This is easy enough to do but the question is how do we get the receivables account straight after that. Right now we are holding on the check until we have a process