How to Refund a Partial Payment
In order to refund part of an original payment, you must undo the allocations by clicking the red X to the right of each invoice as shown below. Once all allocations have been removed, you will be presented with an option to refund the payment. At that point, you can apply another payment, minus the amount you want to refund.
It is only permitted to do any type of refund in A/R if the payment has no allocations, or if allocated, everything on the payment is first unallocated. Then, you can only refund the entire payment, not a portion of it. It is recommended to inform the cardholder for a matter like this, as it is possible this may be seen as suspicious activity.