Hey there.
I’m so sorry to hear about this. It’s not easy, watching our pets go slowly.
After Dr. Magnifico posted about this awhile back, I had a list of Things my cat liked to do. As the list shrank, I knew we were closer and closer to letting him go. My list included eating, drinking, cuddling, playing, etc. I would make a similar list for your dog, and monitor based on that.
For the puppy, I would honestly keep them separate when pup is acting like a puppy. This could be as simple as tethering him to someone when he can be supervised (something I recommend anyway for the first 6 months to help with housebreaking and general naughty behavior) and crating when he can’t.
I suspect that this is related to allergies and therefore the answer lies in helping the body from the inside out versus trying to get topical products work for the outside in.
Please talk to your vet about the many options we have for treating atopy in dogs.
You may also need an oral antibiotic or medication for over abundant yeast.