Recording A Refund Without Going Through The Processor
If a payment has been made sometime ago, i.e. more than 90 days, most processors do not allow a refund. In these cases, you will have to send the refund to your customers in some other ways, like sending them a check, or wiring them the refund.
After you manually send the refund, record the transaction in Payment Center by going to the payment record and clicking the Refund button. On the next page, tick the box highlighted below:
The above will simply record the payment and not try to issue a refund through the processor.