So, you refunded the customer without cancelling the order and issuing it through the case? As it stands, eBay doesn't know why you refunded... they still see an open order. I wonder if it's a situation that you'll have to actually contact eBay, but possibly another poster will know of how it can be fixed without them.
If you do have to reach out to them, I can tell you that I've had success with a message on the eBay facebook page. Quick, concise, intelligible emails come from qualified C/S who have the ability to and the resources to help you out. Good luck.