Thank you for submitting a request to the product development team. 

My work around is to create a credit memo in the amount of the overpayment, send it to the customer, then go back and delete the credit memo. When they pay their next group of invoices and use the credit memo, I will match it with the overpayment that is sitting as a credit on the customer account. It's kind of a clunky way to do it, but it's all I could come up with. Hopefully everything will reconcile out in the end. 

Thanks for your response.