I would head to a vet school/big clinic. You need a good workup, with a good x-ray machine and ultrasound. Then, you and your vet will be able to follow a plan to treat the problem. Vet schools/big clinics are usually well set up to deal with unusual problems. They have pavement for jogging the horse, good lighting for examining him, lots of vets so he can be observed from several angles simultaneously, video cameras to observe him on a treadmill, good x-rays, expensive ultrasound machines and MRIs. You should be able to get a lot of information so you and your vet can work on treating the problems so the horse can be your eventer.
viney, I'm sorry you are going through this. I am with the many others (frugalannie, SEPowell etc) who recommend a thorough veterinary examination/diagnosis by a vet expert in this to find out exactly what is going on with your mare.
Then you can follow the best course of action for her.
op said she has been trimmed for years by a "natural hoof nazi" and now her feet have bad angles <---synopsis on my part
does anyone else think it super weird to hear farriers call themselves "natural hoof or natural shoeing" farriers? this has always been a major red flag for me when choosing a farrier- what the heck else other kind of farrier is there? artificial faux alien hoof farriers? it seems the whole purpose of a farrier is to take a horse's natural hoof and protect if not improve it! IME when asking a "natural shoeing" farrier what he means by that it turned out to mean that he really didnt know how to put shoes on and just knew how to trim from taking a 6 week course ONLINE...omg scary. not to hijack thread or start any drama but nothing can screw up a horse faster than a bad farrier. be careful and be skeptical- its worth it!
I really do hope for the best for your mare viney! I know there's nothing more heartbreaking that having your baby hurt or lame! Jingles for quick growing feet!
Am no expert but will share one experience and what I believe I gleaned from the vets and articles I read at the time.
I had a yearling with ocd lesions in both front fetlocks. I would see something off when she was trotting in the pasture but when the vet would come she would appear fine. So we finally took her in for films.
From what I understood from the vets (and the surgeon flew down here from Cornell to do the surgery because it was his specialty) similar lesions can and do occur in other joints, including the stifles, however often do not manifest as a lameness until the horses go to the track and into work. I know you are linking the being off to the hoof trims, but without films you could be missing something else, and ocd such as my mare had is often bilateral.
On the hopeful side, my mare had surgery and had never been lame since (she is now nine). And I don't believe it is just because they caught and treated it when she was young. At the time she was at the clinic for the surgery they had a high level jumper in for the same surgery on his stifles and his prognosis to going back to jumping was very good.
All that said, I freaked out slightly when the above mare was started under saddle because she had 'loose' stiffles -- the vet was not concerned at her age and fitness -- but I insisted on films because we had not taken pictures of the stifles when we did her fetlocks. I knew ocd can be in multiple joints. Her stifles were fine and it was just conditioning she needed. But for my piece of mind I wanted the films.