Don't worry too much. Soft stool for a long period of time can cause the anal glands to not empty properly. Ask your vet to show you how to empty them. The thing is, your dog went from a commercial food with stool hardeners in it to a natural, more dense food with no stool hardeners in it. It's going to take a while for the stool to normalize. 3 cups is a lot of food though... How much does this doggy weigh? The feeding guidelines are terrible. Most people on this site don't follow them at all. Dogs tend to become overweight if you follow those guidelines.
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