Allow refunds and credits to customer accounts
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.