The last time this happened to me, eBay wasn't managing payments and all that happened was the transaction was cancelled, but the PayPal funds were never reversed or even contested - I assume because the person just claimed someone else used the eBay account to make a purchase, but they never claimed someone else used their PayPal account (or other payment source) to pay for that purchase. (It was such a weird claim to make at the time, like who hacks someone's eBay account just to buy something, when you can just check-out as a guest, but I digress). 

The timing of the transaction to the message aside, now that ebay allows people to put a card on file and automatically pay for items, plus they have much more control over the funds once paid, they might try to reverse the payments, but like springy mentioned, this should have the same kind of protection of any other "unauthorised use" case (though they don't actually even have specific policies for this kind of scenario, the unauthorised use comes the closest). More so, even, because a hacked account can easily be argued to be a security failing on eBay's part, if not ignorance / complacency on the buyer's part, so why make sellers pay for that? Oh, that's right, the big corporations don't like taking liability, and even in cases where the buyer clearly contributed to the circumstances (like falling for a phishing email), if you make them liable for their mistake, they might not spend money on the site anymore, so sellers it is. ‌‌

If they have reversed the funds and you would have qualified for protection under any other circumstance (and it sounds like you would), I'd get on chat and ask them why it wasn't applied. The transaction being well over 2 months ago has the most relevance here - it's an automated email, of course, and seems to assume someone with a hacked account would notice immediately if there is fraudulent activity, and in the obvious absence of that diligence (lol), surely eBay's "fraud detection" is robust enough to be a bit quicker off the mark, too. (lol, again). 

Good luck.