What 'shots' are you referring to? If they were vaccines, you may want to consider holding off on those until his immune system is stronger -- but keep him protected from other dogs/outside etcetera. Maybe you meant some other kind of shots.
When they're retesting him - are they doing skin scrapes only? Bc w/ resistant mites - they will often BURROW under the skin and aren't visible on scraping...burrowed mites can only be found via biopsy of the skin. Maybe a biopsy would tell you something...?
So sorry he's going through this, poor little kiddo
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