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.