If you went to PP and refunded the payment made, it shouldn't be a problem - when ebay refunds in this situation, it takes the money from THAT transaction and gives it back to the buyer. Ebay should recognize that the refund has already been sent and maybe will generate an error - most likely not. If it's been more than a few hours, check PP and make sure that all looks right.
If you simply sent the buyer money in a new transaction (that is, you didn't opt to undo the previous transaction, you instead created a new one) then you have a problem. I suspect the only way to fix it would be to contest the refund - it isn't actually a refund at that point - it's a payment and every pp payment needs to have a tracking number associated with it.
But it should all be clear by checking your paypal account