Hi TH1833,

Thanks for posting in the Community!

You can categorize the duplicate payment as a bank deposit and use the Accounts Receivable. Then, link the payment to the invoice by manually receiving payment against the invoice. Here's how:

1. Click on the Transactions tab.
2. Click on Bank transactions.
3. Locate and click the payment, select Deposit in the Type of transaction. Under Account choose Accounts Receivable.
4. Click on Add.

Then, let's go to the invoice you've created and then click on Receive Payment. Under Credits select the Deposit to apply the payment. Here's how:

1. Click on the Sales tab.
2. Click on All Sales.
3. Locate the invoice and click on Receive payment.
4. Under Credits make sure the deposit is selected to link to the invoice.
5. Click on Save and new.

Check this link to learn more about Handle customer refunds in QuickBooks Online.

Drop by again in the Community if you have further concerns. I'll be around to help you.