Thanks for hopping into the thread, @rteshiba.

I'm happy to help out here. To make sure this customer's Accounts Receivable doesn't have a duplicate incoming total, you can record a Refund Receipt. This way you can record the returned payment. Check it out:
 

1. Go to New (+), then Refund receipt or Give refund.
2. In the Customer ▼ dropdown, then pick the customer you want to refund.
3. Select the Refund From ▼ dropdown, then select the bank you deposited the payment for the invoice too.
4. Add all products or services the customer returned in the Product or service column.
5. Make sure to fill the quantity, rate, amount, tax, and other fields accordingly, then hit Save and close.
    

You can also check out these resources for alternatives to record a returned payment:

• Enter a returned or bounced check using write check
• Enter a bounced check using a Journal Entry

Let me know if you have any other questions by giving that Reply button below a click. I'll be here to help.