This does sometimes happen, but when it does, there is nothing which can be done through eBay, as that transaction was closed with a refund.
Send the buyer a message. Say you are happy to see that tracking has now shown delivery perhaps here you can apologise for the lateness of that delivery. Ask for them to please now repay you for the item.
This can be done with the buyer sending you a Friends and Family payment through PayPal, they will need a PayPal account for this, Or, you an send them a PayPal invoice for this amount. They do not need a PayPal account for this and can pay you there by various card payments.
One tip, if PayPal is used email addresses are required, make it very clear in eBay messages the purpose for asking for the email, so it cannot be mistaken for the beginnings of an off eBay sale. Or, they can send a cheque to cover the amount, whichever suits you both. Nothing can be done, unless you take a legal route, to enforce the buyer to pay, but most people are honest and do not want an item for nothing.
Don't chalk it up as a loss, if the above doesn't work, and you say the item was of value, then you may wish to take a legal route to regain the money.