The white calcified areas in your horse's ears are likely Aural (ear) Plaques. Your vet is correct in that they are very difficult to resolve and can likely only be managed. Some horses appear tender when these plaques are present, while other horses doesn't seem to be affected by them. However, just trying to examine and medicate them makes some horses ear shy.
What causes these lesions is not totally understood, but biting flies make them worse. Treatment should include managing biting flies with fly masks that have ear covers, applying fly repellants like "Swat" to the ears and not clipping the ear hair if possible. Also, using a moisturizing cream or just vaseline on the lesions to soften and remove the white granular material is generally recommended. The lesions will usually remain as pink areas in the ears and will likely need to be treated at some interval to keep the calcification under control.
A potential new treatment is the use of Aldara cream on the lesions since some evidence may link the cause of the aural plaques to a virus. The main drawback to this treatment is the cost of the ointment and the need to treat for at least 1-2 months.
