Why is my dog losing hair with painful skin? No lesions, on a jak inhibitor

Hi! I’d like to preface this by saying I work in a vet hospital as a receptionist and VA when needed. I’m fortunate to be able to take my dog in at the slightest concern, and I have the resources to be proactive. That being said, has anyone seen this before?

I adopted my almost 4 year old chihuahua x bully (dna tested) last year. After a couple months with him, he started experiencing excessive shedding and patchy hair loss on his dorsal neck, withers, and a little on his rump. He wasn’t itchy, but we started him on apoquel. Very boring skin cytology via tape prep and impression, we also did a skin scrape to no avail and a dtm which was also very boring. Around this time he also had some irritation of his ears, but no discharge, odor, and the cytology was boring. We treated with mometamax because there was a little yeast and bacteria so why not and it appeared to help, but follow up cytology was the same as the first which led us to believe that was just his normal biome. I started him on twice weekly baths with duoxo pyo shampoo and use the pyo foam after. Finally, after 1.5 months without real improvement I tried melatonin based on some information about it potentially helping with alopecia. His hair did begin growing back and felt softer than before too. We kept him on that for months along with daily apoquel and weekly baths with duoxo calm and the pyo as needed. Ear flushing with EpiOtic prn as well, however he doesn’t like it and it doesn’t seem to improve his ear discomfort anyways. Zymox with hydrocortisone does offer him more relief.

Fast forward to now, we eventually discontinued the melatonin and there were no changes. When i try taking him off Apoquel he’s itchy and his skin gets inflamed, so we keep that up. He’s on an omega 3 oil and Glandex as well. We’re at the year mark from his last flare and his hair is shedding excessively leaving patches, and he was painful. He yelped at the touch when I pet his neck, and would shiver in pain after. I was worried about a neck injury so we had him seen. His neck was inflamed where the rest of his body was his normal pink. He was also shaking his ears more but in the reluctant, ears pinned to the side way he does when his ears hurt. Normal tape prep again, normal ear cytology. His doctor did a trichogram and all hair follicles appeared to be in the shedding stage but otherwise boring. We’re trying pred now and within an hour the inflammation is down and he’s enjoying pets.

Next steps for him look like sedated otic exam because he won’t allow a good look while he’s awake. Possibly diet trial and allergy testing, although I’m less suspicious of that as he has shown pretty clear and immediate gi upset with any feathered protein, but has done well on PPP sensitive skin & stomach. I’d be willing to do it, however this would cause difficulties with his training and I’d like to avoid it if possible.

He has never had a hotspot but I am very proactive and have started epsom salt paw soaks during his baths. I have genone spray for the times he messes with his paws and that has successfully warded off any actual skin infection.

If we weren’t able to successfully treat him, I’d take him to see a dermatologist, but at this point it feels like a lot of money to answer my curiosity. I’m not against this option either though and would 100% take him to see one if we weren’t able to keep him comfortable.

Has anyone seen a case like this? Any additional thoughts on diagnostics we haven’t tried or discussed?

Thanks so much for reading this far and any insight you have!