I'm so sorry to hear what you've been going through - wow, you've really been through the ringer! Sounds like a pretty complex situation that would require an amazingly competent NM dentist that is working closely with a team of others professionals, such as PT and chiro so that they can all be comunicating closely to figure out and treat your issues in conjunction.
I am not an expert and I really don't know anything about hypermobility syndrome but I want to share the little that I can in the hopes that it might be helpful. One thing I've learned is that issues in the jaw often goes hand in hand with misalignment in the body. I believe this misalignment can exacerbate pain issues and the misalignment in the jaw - working together to form a nasty vicious circle. As a result, I think they both need to be treated simultaneously by professionals why are extemely experienced and consulting with each other.
My NM dentist works very closely with a chiropractor who also specializes in TMJ issues. When my splint therapy didn't seem to be relieving symptoms at first, he sent me immediately to work with this chiro. My body wasn't straight at all - hips twisted and one lower than the other, one shoulder much higher than the other. You could tell just by looking at me. At first my body kept slipping back into its original misalignment, but as splint therapy proceeded and I had the chiro straightening me many times over several months, I finally held. I still need to go back from time to time as I'm now in braces and the changes in my jaw are still affecting my body. I also needed an atlas adjustment to finally get straight. It was very twisted, as it is for many folks with TMJD. My NM dentist felt that straightening my atlas was key in treating my jaw issues.
I'm wondering if this type of treatment, done by a really well-trained, well-reputed NM dentist/chiro team would help you as you mentioned that your body was holding the changes your PT made for a while. I'm also wondering if the changes in the body need to be accompanied by changes in the jaw to be permanent.
Did you see a physio that specializes in TMJ/orofacial issues or one that understood hypermobility syndrome or both? I went to a regular physio and didn't get any help whatsoever but once I went to one that specialized in TMJ, she was really helpful. I have central sensitization so it's so easy for my pain to be exacerbated by treatments - I really needed a PT (and chiro) who fully understood the nature of this so that they didn't cause me more pain with their treatments. I imagine you might need that as well with your hypermobility syndrome.
Well I really hope you get some relief soon. It's a long, strange and difficult road but don't give up. Keep trying until you find relief. I was mired in pain with so many dentists and professionals who were not helping, causing more pain and drying up my wallet. Finally, I did a ton of research to find the best NM dentist in my area with tons of experience and post-grad work under his belt and I'm now on the road to recovery.
Hoping you find relief soon! Best of luck