I just spent an hour on chat support for this very reason.
Here is what you do.
1) Create a new check (see attached example).
Payee is the client/job.
Category is Accounts Receivable
Amount is refund amount
Customer is client/job.
2) Go to client's payment and this new check should now be sitting in the list of Outstanding Transactions. Check the box next to your new check and the overpayment should zero out.
