eBay hasn't ever had an official policy that provided for refunds of fees when sellers give partial refunds to buyers, though in the past it could be requested, and now their official policy is that no fee refunds are provided.

The best thing to do is try to make it as clear as possible that any advertised combined postage rates only apply when items are checked out together, so as to encourage as many as possible not to check out items separately. Then if people do and you want to refund excess, provide a refund minus the eBay fee charged (this is how I tend to deal with it - the only time anyone has ever complained is when they assumed I was refunding for items I couldn't / didn't supply, I'm on managed payments now and I assume selecting "postage discount" as the reason for the refund communicates it a bit better as I haven't had anyone go off on me about that since I was switched over 🙂 ).