You almost certainly needed to send each pair of shoes separately so you had a different tracking number for each one.
If you received the shoes as one package (a single transaction) and only had to open one case for return, then you should have been refunded for the whole transaction, or both pairs.
Otherwise, you can't prove both pairs were returned.
Probably worth a chat with Ebay to explain you have returned both pairs and only been refunded for one. They may help. use the link below for an online chat or a callback.
https://www.ebay.co.uk/help/eua?id=5275&mkevt=1&mkpid
"There are two ways to be fooled. One is to believe what isn't true; the other is to refuse to believe what is true.”
Søren Kierkegaard, Danish philosopher (1813 - 1855)