I’ll try to stay off of my soap box about getting a puppy (especially paying for one of the “designer” non-breeds) and not having planned ahead for unseen expenses.
If you haven’t already, I would recommend placing the puppy on an adult food. Small breeds mature more quickly than large ones, and at 9 months he will do fine on an adult diet. The reduced fat and calories may help. Make sure that it’s a high quality diet, and you may even want to look for something labeled for “sensitive stomach”. (Be careful about bouncing around among the various proteins [beef, chicken, lamb, kangaroo, etc] – if he develops a food allergy, you’ll have a hell of a time finding a novel protein [one that he’s never been exposed to] that his body will not react to.) Any diet change should be gradual, mixing the new diet into the old in increasing increments.
Make sure that his monthly heartworm prevention includes a broad spectrum dewormer. Dogs can be re-exposed to intestinal parasites every day if they are coming in contact with contaminated soil. Unfortunately, none of the prevention on the market will prevent giardia, but you certainly don’t want to miss something easy like worms.
Has the vet retested his stool sample for giardia? It can be difficult to see on a slide preparation – in many cases, giardia is diagnosed through the process of elimination. If the test is negative for worms, and flagyl makes it better, it was probably giardia. (There is a snap test for giardia, but I’m not very familiar with it – it may just test for exposure). Ask your vet about an extended course of flagyl (21 days rather than 7), but make an informed decision – ask your vet about the possible side effect of metronidazole (flagyl).
The probiotic is not a bad idea to continue. Some people think it helps, some don’t, but it doesn’t hurt anything to try.
Be very strict about his diet. No people food, no liver treats, no cow hooves (it’s not unusual for dog treats to have bacterial contamination). If you get everything cleared up, you can gradually add treats back into his diet, and if his diarrhea reoccurs, you may have a good hint as to what caused it.
You need to keep in mind that medicine is not math – there are no hard and fast rules. Your vet has to act more like a detective trying to solve a mystery, often through the process of elimination or even hunches based on years of experience. The number of things that can go wrong with a living being are literally endless, and it’s possible that you may never have an answer.
We saw a cat this week in our Internal Medicine specialty that has had diarrhea for 10 years. After bloodwork, x-rays, endoscopy and biopsies, the best answer that we got with was IBD, irritable bowl disease, which gives us an idea of how to manage the disease. There is no cure.