The of refunding a prepayment is to simply apply the credit to a "treatment", and then perform the refund as usual. You can do so with the following steps:
- Create a treatment and use item "Adjustment" (if no such item, create one for it, click here for instructions.
- Update the Adjustment treatment item to the amount you wish to refund and create the invoice.
- Apply the credit to the Adjustment treatment (make a payment using prepayment).
- Go back to Treatment tab, on the cog button of the Adjustment treatment and click Credit note or refund.
- Go through the prompts and manually refund through with desired payment type.
And done! You've just refunded a prepayment and this will reconcile nicely with your books.