It’s normal for buns to scratch their ears sometimes of course! 🙂
It doesnt look too bad to me, but it could still be fur mites. It could also be related to shedding, it’s not uncommon for buns to get some “dandruff” when they shed. I think I’d just keep an eye on it for now. You can brush the ears with a very soft baby brush to help him get rid of the skin flakes. If it gets worse, if he develops scabs or sores, mites could be the cause. Revolution (selamectin) is the best treatment for rabbit mites. It is prescription only in most places, but since your bun has been treated for mites before, maybe your vet could just let you buy some Revolution from them without a vet visit.
(And while we’re on the subject of antiparasitics: Never use any compound containing fioronil on a rabbit. Fipronil is sold OTC as Frontline and several other brand names. It’s fine for cats and dogs but its deadly toxic to rabbits. End of public service message!)