I dont suppose when he eats his ears dip into his food? Maybe there's food residue which he is trying to get off - even if thats not the case now, perhaps that's how it might have started?? Difficult to know what the reason is, I'm afraid, so I think I'd try and focus on the prevention in a case like this - in addition to the above suggestion, perhaps you could try to prevent him from chewing his ears by buying something to keep his ears up (only to be worn when you are around) e.g. a snood, or maybe a scrunchy - just to see if this will break the habit?
Otherwise, in general, is he okay about having his ears touched/ stroked?