I have the same problem and did what was recommended. After doing so, it shows up as a receivable. I zeroed out the payment, but the customer payment screen still shows the payment amount. The payment also shows up on my bank register. When I try to delete the payment, I'm going in circles with it not letting me. It tells me to delete the payment from the deposit. Go to the original payment transaction to edit it and redeposit the payment

To delete a customer payment, follow these steps:

1. Go to the Customers menu and click on Receive Payments.
2. In the Receive Payments window that appears, select the Previous button until you find the payment.
3. Select the Edit menu and click on Delete Payment.
4. Click OK to the warning: Are you sure you want to delete this transaction?, then select Save & Close.

You can also delete the payment right on the invoice's page. You can delete the related transactions associated with it before deleting the invoice itself.

Here's how:

1. Open the invoice.
2. There are two tabs on the right panel of the Create Invoices window.
3. Go to the Transaction tab.
4. Under the Related Transactions, it will show the deposit you use as the payment.
5. Open each transaction and click on Delete. 

You can now delete the invoice once you're done.