Manually enter the chargeback as a refund using the Cash, Check, or Direct Deposit options without sending a refund request back to the gateway. This is effectively matching the current balance of the customer after the chargeback has taken place.
Leaving good information in the reference field will save some reporting headaches down the road.
To prevent a specific outstanding invoice from collecting again, flag the invoice as disputed. Alternatively auto-collect can be turned off for the customer in order to prevent the system from performing any further automated collections.
Ideally, there is a dispute process with either the gateway or the bank in order to provide justification for the credit card charges.
In the gateway, Fusebill uses the Customer's Fusebill ID in the invoice field. This is in part because Fusebill works on an accrual basis. The Fusebill ID indicates which customer balance it is paying off. Invoices and historical statements could potentially be used in this dispute process.