The best way to show a return on an invoice is to add a new line item called "RETURN" and include the details of which item was returned in the line item description and put the negative dollar value of the returned item so it's like you're subtracting that item from the invoice. This way you have a record of what was returned. If you save the invoice with a total lower than what your client paid, the overpaid amount will go to your credit balance in the project.
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Watch this video on credits and retainers: 

You need to create the credit from the invoice you took the payment on and then that money will be in your credit balance for the project and you can apply it to any other invoices in the project.