How did you record the original prepayment. If you received a payment, it would create a credit for the customer's balance. In this case, when you go to "receive payment", you should see a credit balance at the bottom of the screen. Check off the open invoice. You will get a warning, but ignore it. At the top, go to discounts and credits and apply the credit to the invoice.
If you recorded the original payment as a deposit to a customer deposit or liability account, you will need to create a journal entry to move the payment. Debit the liability account and create accounts receivable and include the customer name in the field on the journal entry. Then follow steps above to apply the credit.
