Locate the payment check. What account is it tied to?

The From account should be Accounts Receivable. Edit the check to change the account if need be.

You will probably get a message about the credit, but that is ok.

Then go to the Open invoice Report.

Choose the customers invoice and open it.

On the top there should be a capability to Apply Credits.

Apply the credit to the invoice to clear out the invoice, but you will not have effected the deposit or the payment amount.