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Has your vet been in contact with Dr. Gonto? (email@example.com) Dr. Gonto is the one who developed the Fanconi protocol and is more than willing to work with vets.
As far as the supplements, if you join the Yahoo Fanconi Dog group, a whole host of pill hiding ideas that have been successful with picky eaters is available. And you can always pill by hand or using a pill popper (available at Petco and PetSmart). What worked best for us was liver sausage or braunsweiger (sp??). It has a sticky consistency which makes it hard for them to eat off without swallowing the pill. We did 1 ball without pill, one with, then a couple more without, then another one with a pill, etc. Also, if you give her pills in the presence of the other dogs, sometimes the competition will encourage her to take the pilled treats.