We have a rescued OTTB (now rising 5) who had a terrible ear shy problem. Clearly he had been ear twitched at some point and any attempt to touch, rub, hold, look at his ears would result in evasion and fear. I tried desensitizing him, but hadn't been able to spend enough time to overcome the memory.
He, being a Thoroughbred, is also thin skinned, so we had major fly problems this year and we bought him a new fly mask with ears. He'd been wearing a "regular" mask (no ears), so he didn't really react to the new mask.
Now, no ear shyness (took about 4 days). In fact, he likes getting his ears rubbed!
Just a new tool in my training bag.