Keeping the Funds in an Over-payments Account
To track the over payment you can enter a Purchase with this supplier. Instead of coding it to an expense or cost of sales account, code it to an Asset: Over-paymentsaccount. This helps you track money that has been overpaid to your suppliers.
Later, when you buy goods from this supplier, you can enter that transaction normally. You can also enter an extra line coded to that same account or do this as a separate (credit or adjustment transaction) for a negative amount. Then, when you close this Purchase transaction by applying a payment, it is for a smaller cash amount (by the amount of the original overpayment).
