Is this a possible solution to this issue:

1. Go to your menu Banking then Write Checks.
2. Choose the appropriate bank account
3. Choose the appropriate check number and date.
4. Choose this same customer in the Pay To The Order Of field.
5. Fill in the amount of the overpayment you wish to refund.
6. Very important to choose Account Receivables in the expenses tab near the bottom of the screen.
7. Click Save & Close.

Note, if you get a warning that states "Please choose a customer when using an Accounts Receivable account as a line item" then choose this exact same customer in the field (within the same Expenses tab off towards the right) called Customer: Job if this field does not exist, then you may have to change a company preference setting.

Now, If you look at this customer's AR balance, this check refund should be reflected here, however, you still need to apply this check refund to the overpayment credit; otherwise, these two line items will always appear as open. To do this:

1. Highlight the customer in the customer list, then click on New Transaction (at the top of the customer list, not in the company menu list) and choose Receive Payments.
2. Within the Receive Payment screen:
   - Don't fill in a payment amount; instead, just highlight (not checkmark) the outstanding check payment amount as listed in the open invoices list, then click on Discounts & Credits listed as one of the button items towards the top.
   - Find the Available Credit which is the overpayment amount and be sure it is check marked. click Done.  

You will now notice there is a new column called Credits and thus the NET of the Amount Due + Credits is equal to zero.