I have been rubbing and folding my ears all my life. I'm 27. It is a comfort thing. I do it the most when I need to relax. It is honestly an amazing feeling I don't know why.. Lol. I always wondered why everyone didn't do this!! I've had no issue really from doing this. I do have less cartilage in my upper ears, compared to anyone I've met and sometimes if I fold them for too long, they can hurt a bit, but that's it :)
Maybe, with the ears, it's just a habit she has? My son is 7 and he's always played with his ears, particularly when he gets excited. It worried me quite a bit when he was younger, but we've all got used to it now. When he does it, he sort of pinches and rubs them, sometimes he ends up with scratches on his outer ear if I don't keep his nails short!
Are the two connected in your daughter's case, ie did they start at the same time? If so, I'd take her back to the doctor if it's worrying you.