I recently discovered a payment was recorded twice in our quickbooks online account (due to an integration between qbo and another website we use.)
The first payment was applied to the correct invoice. The second payment was applied to other invoices for the same customer. This resulted in two invoices being marked as paid that should not have been and also the creation of an entry in an "Unapplied Cash Payment Income" account.
This all happened in our previous fiscal year for which we have already closed our books in quickbooks online. It is also affecting this year's P&L because of the amount in our Unapplied Cash Payment Income account that rolled over into this year.
If the payment is more than the invoice amount, our system will automatically create a credit to the customer. The amount will be added to the Unapplied Cash Payment Income account.
If the invoice should remain open, you can unapply the payment. Here's how:
Open the invoice.
Under Payment status, click the 1 payment link.
Click the date link to open the payment.
Under Outstanding Transactions, uncheck the invoice, then click Save and close.
A pop-up message will appear, click Save as credit.
You'll receive a message, "The transaction you are editing is linked to others. Are you sure you want to modify it?", click Yes.
This will create a credit to the customer. Though, if the invoice should remain close, I suggest consulting with your accountant on the best way to handle this. They might let you create an offset or journal entry. They can help you categorize the accounts since this payment was recorded last fiscal year.
You can always get back to me if you have other concerns. Have a great day!