Did your client pay too much in error? Or perhaps you have agreed upon a full/partial refund and are unsure on how to handle it?
All payment processing would be completed by your merchant account (Authorize.net®, PayPal™ Business, Stripe™, or Square). This means that you will want to refund the client directly from within your merchant account.
You can then adjust an invoice to reflect the refund by navigating to the invoice in question, pressing "Record Payment", and adding a negative dollar amount transaction (matching the refund amount) to balance/zero out any overage.
Your invoice will now show the amount was returned to the client, meaning the invoice now has an open balance.
If you would like the invoice to stop showing as due, (ex: Your client cancelled services and their deposit was returned), you can add a line item such as: Cancelled Services, totaling the amount remaining, listed negatively:
KeywordSearch: Invoice, Refund, Bookkeeping, Manual Payments