Paypal refund not showing

I had an international buyer pay for an item before i was able to send an invoice. The buyer ended up not paying enough to cover the 1st Class International shipping so I emailed him and refunded his payment through paypal in the hopes that I would be able to send a new invoice. I have done this in the past and it works fine. I refunded the payment through Paypal (and Paypal is showing that the refund is complete) but now ebay is not letting me send a new invoice and is still showing that the item has been paid for. Marking the item as "payment not received" does not let me send an invoice either. Any idea what's going on or what i might be able to do?? Thanks in advance!