Hi Cadicka,
Thanks for reaching out.
If the excess of the payment was showing as a deposit for the customer, then you could apply the deposit to the other invoice and act as a payment to have it closed. Here is the help article Customer overpayments and double payments that will serve as a guide. The customer's overpayment that was converted into credit should be sitting inside the "returns & credits" under the sales register.
Let me know if you require any further assistance with this. I'm happy to assist you.
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Cheers,
Genreve