Navicular syndrome is a catch-all term for a variety of different types of injury to the back of the foot (e.g., caudal heel pain or foot pain). Veterinarians diagnose most navicular syndrome cases based on a lameness exam with hoof testers, diagnostic nerve blocks (anesthetizing the heel and sole of the foot), and then radiographs (X rays) of the foot and navicular region. Sometimes the radiographs show changes to the navicular bone and sometimes they do not. The ultimate method in confirming navicular syndrome diagnosis remains MRI.
Veterinarians generally approach navicular syndrome/caudal heel pain treatment in a stepwise fashion. The initial step is decreasing inflammation within the foot using non-steroidal anti-inflammatories such as phenylbutazone (Bute) or firocoxib (Equioxx). This is followed by making shoeing recommendations. In your case, your vet has prescribed a particular shoe with emphasis on providing a rolled toe. The reason for the rolled toe is to provide an early breakover point for the foot. By doing so, the stress on the deep digital flexor tendon (DDFT) decreases and, thus, the stress and/or inflammation on the navicular bone and surrounding region decrease as well. This is a very important part of treating horses with navicular syndrome.
The next step, if the shoeing is ineffective, is to discuss intra-articular or joint injections of corticosteriods. These provide a potent local anti-¬inflammatory effect for the joints. Veterinarians can inject these medications into both the coffin joint and the navicular bursa (sac of fluid around the navicular bone that helps cushion the DDFT against the bone). There are additional options beyond the joint injections, but given that your horse is managing well with the shoeing changes, I will limit the discussion at this point.
In general, horses such as your mare will need a veterinary-prescribed rest and rehabilitation program based on the exact diagnosis--arthritis, torn tendon, injured ligament, etc. These rehabilitation programs often consist of several months of measured exercises for your horse. Treat this injury like any other athletic injury, and with adequate time healing should occur. This is the best way to prevent future problems.