Good luck. I'll be curious to see what you find out too. I hope you can get him some relief.

If the dog had allergies in the past, he still has them. The 1-year course of shots (immunotherapy?) then a different course of treatment (the holistic route) kept symptoms at bay for as long as you were treating. I don't doubt that he showed improvement while being treated, including all symptoms going away, hair and skin returning to normal, etc.

What's worth remembering with allergies is that they cannot be cured. If he is allergic to something, he will always be--and may even develop new allergies. No single course of treatment will make him allergy free. Treatment can only suppress symptoms for as long as the treatment is being given--or, in the case of a seasonal allergy, for as long as the allergen is in the environment. Even immunotherapy, which is the closest thing there is to a "cure" for allergy requires maintenance shots for life. It's not like an infection that can be completely eliminated from the body with a course of antibiotic.

The presentation on the body (itching of muzzle, feet, ears, arm pits) doesn't always make logical sense. An inhaled pollen in a person (like hay fever) might make us sneeze, which makes sense to us because that's where histamine receptors are located in humans--in the nose. In dogs, when they inhale an allergen, the reaction might be that their arm pits itch, or their feet, or their face. It's just a difference of where their histamine receptors are located.

The point is, that an itchy muzzle doesn't necessarily mean that the source of the itching is muzzle-related any more than itchy feet mean the dog stepped in something that caused an itch.

Best of luck. give him a scratch from me!