How was the payment made?
If the purchase did not occur through ebay and you just received a direct payment through PayPal, in order to avoid any problems with eBay, I would enable make an offer on the item and ask the buyer to send through the offer via the item listing and offer function, for the price they paid. (Advise them that no further payment is required, you just need the sale to be officially recorded on eBay).
Then I would accept the offer and immediately mark it as payment received.
The reason I suggest this is that if no sale is recorded through the usual means and you just end the listing, eBay may hit you with a policy violation for selling off-eBay, and charge you the fees anyway (they scan messages via bots and can now connect the dots between an inquiry coming through on a listing and that listing being subsequently ended).
