Thanks for the question...this is a nasty and painful disease. The treatment is varied and there is really no known 'cure' per se.
1- Have all the loose nails
removed under general anesthesia. Get the pain over with.
2- Prednisone/steriods can be used short term for inflammation and pain reduction but recently we have started just using Metacam an NSAID and Tramadol a narcotic pain med.
3- High doses of Omega 3 oils: 200-400 mg of EPA per 10lbs of body weight. You need to get the EFA packets of daily dosed oil...not the capsules because you need a lot of oil and a high dose. Do this daily. For a shepherd I'd be giving him 2500-3000 mg per day at least.
4- Doxycycline or Tetracycline: doxy: 100 mg twice daily. Tetra is 500 mg three times daily.
5- Niacinamide: (go the health food store and get this) 500 mg 3 times daily.
Confirming this diagnosis can only be done with a biopsy...or removal of 1 complete digit...amputation of the digit.
I have a boxer
I am treating now and am actually considering removing-declawing all of his toes in order to lessen his pain and stop this disease...so as I said it is a difficult and frustrating disease.
Best of success to you and your dog.