It's up to the buyer now either to a) return the item under eBay's money back guarantee (which they can do if it arrived after the latest estimated delivery date), or b) keep it, and repay you by some other means e.g. by PayPal, bank transfer, cheque.
You will have to hope that your buyer is honest, because eBay gives sellers no support when buyers claim a refund, and then keep the item as well when it arrives - even with tracking proof of delivery.
It's absurdly over-generous anyway to allow buyers to claim a full refund if an item is even a day past the estimated delivery date - no delivery service does this. eBay could so easily amend the user agreement to require the buyer to return either the item or the refund, but they don't. It's almost as though eBay simply desn't care about buyer on seller fraud.