Glad to hear Atlas is doing better. It will take time for his tummy to heal and for the bacteria to get better established. For bacteria to flourish in the gut, it needs to be inflammation free and a diet with plenty of soluble fiber. It was after my girls were eating the Natural Balance Kangaroo and Potato for several months that I was not able to transition them to a new food without adding the kefir, even though one had been getting a good pet probiotic every day. It is a good food as far as digestion, but in my experience was not good for promoting gut health. (I never had a problem transitioning foods prior to the NB).
You may want to consider Purina Pro Plan. If you take a look at some of the threads on here, there have been several people with large breed puppies that were having poo issues, and they said their dogs do better on Pro Plan.
Good luck with the new vet and hopefully he/she will be able to help get Atlas on a more appropriate diet.
