The only way he can get his fees back from eBay is to win an NPB case (or get you to agree to a mutual cancellation, but maybe he doesn't know that) - if I had a suspended PayPal account, the last thing I'd be worrying about is getting some fees back, but since I'm not a skanky deadbeat seller I'm not necessarily on the right track with whatever he's thinking. :-D
eBay should remove the strike from your account without too much trouble, but even if not, don't worry over it - the old "three strikes and your out" on eBay are long gone, eBay hardly ever sanctions buyers for non-payment anymore, unless they rack up just ridiculous quantities of deadbeat bidding.
The only harm that CAN come of it on a minor level is if you have two NPBs closed against you in the past X number (forget how many, 30 or 60 or some such) of days and a seller has that as one of their auto-block settings. But, since you're unlikely to accumulate a second strike in that time frame that is also unlikely to be any kind of issue for you.