Allow a refund or credit to be placed on a customers account and a note section so you can denote why there was a refund or credit.

Any new invoices would be billed against it, if you offered a credit.

If it was a refund, you would be able to process this against a paid invoice, so there was a record of what was billed and reason it was refunded.

Additionally here would be an email template to go along with ach of these so you could notify the customer.