The best advice is just to leave them alone. Sure they look terrible, but you will do more harm than good by attempting to remove them. They do not harm the horse and if you mess with them you could cause an infection or something. The best thing to do besides leaving the plaques them selves alone is to fly spray and apply a fly mask with ear covers.
Messing with it or applying stuff to try to "fix" the plaques will lead to a whole other painful host of problems for your horse.