I am not sure if you corrected the the quantity on the original Sales Order so that the inventory would be accurate and now you just have an over payment on the Customers Account showing they have a Credit balance. If this is the case, you can either apply the credit balance (remainder of the prepayment amount) to another outstanding invoice, or apply to a future invoice. However if the Customer just wants the balance of their prepayment issued back to them in which case your company may decide to issue them a refund check, you would go into Tasks, Payments. There is a small drop down selection that has Vendor ID, change it to Customer ID. Pull up the customer ID and complete the screen with the correct amount due them and print a check. Please note the GL account will be the A/R Account don't change it. Now you can go into Receipts, pull up the customer ID and apply the prepayment to the check you just issued. For the Check reference number I would use Refund and the check number you used to refund them. When you apply these two line items against each other make sure the "Receipt Amount" shows zero, because you are not receiving any actual money at this time.
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