Drilling in is one of the only ways to do it. A friends dog had it, she was put to sleep due to quality of life as the treatment had no effect. Personally if it was my dog I would have done the same thing but that is only my opinion and in no way should sway you, listen to your specialist they know best with Aspergillosis. Treating your backyard with fungicide is not a great idea they are very harsh chemicals and really will not make a difference.
Immune problems can just crop up or it can be the genetic draw of the cards. I know runts that have grown up to become bigger and better then the rest of the litter.