Clearing off Advance Payment Balances for POs that have been closed

I have a Purchase order that was originally started through Advance Pay, but was received before the final 2 payments could be applied, causing the order to be on both the Received not Invoiced report and the Advance Payment report. Is there any way to clear up both reports without un-receiving the purchase order?

Enter an invoice for the balance that is left payable on the PO. This will clear both the reports. Then you can apply the payments against this invoice.

Problem is, with the lines on the PO being closed, i cannot allocate the invoice to the Advanced Pay.

Enter the invoice against the PO receipt. Epicor will take care of the advance payments already entered.