Sounds as though not returned properly through a case, but xo long as buyer is happy, I think you can just ignore reminder from ebay.

If money is still being held when seller wants to refund, money would be taken from ebay account if sufficient available, if not from bank account.

Again I assume you do not have an  alternative funding source loaded.. 

Because you refunded outside the system, ebay assumes refund still needs to be made, but I do not think any action would be taken by ebay if you just ignore reminder.