Glad you have had the vet out and are looking at a lameness exam. I hope you find whatever is causing her soreness quickly. Lameness exams can definitely take a while and If available, I'd encourage you to work or consult with a lameness specialist, as their experience can be invaluable when trying to pinpoint subtle lameness issues. I think I spent almost 2x more trying to diagnose my horse with regular vets, before I had the specialist out to find the real issue. I'd also keep record of this horse's chiro treatments and anything beneficial you can note about her behavior undersaddle and in general to help the vet.
The pattern you are experiencing with your horse under saddle suggests that something is wrong and has been persisting as an issue. This, you've already known and have seen a pattern with. As it appears, rest seems to either alleviate the issue or help heal it before riding somehow aggravates it again. What is causing that issue or preventing that issue from healing will take some investigative work. Specifically while riding these factors come to mind: recent saddle fit(which you have already checked), arena footing (too soft, too hard, uneven), weight applied to injured area (circles, arena figures, addition of saddle and rider, etc) and increased flexion. Quite a few horses can be sound on turnout, but show soreness or lameness when on a riding schedule.
Retiring certainly isn't a bad idea if It comes down to it, but retiring as a broodmare may not be ideal for your mare at this time. The extra weight of a foal could exacerbate the issue further, where the primary issue hasn't been found yet. Hopefully, your vet will be able to quickly find the issue for you so that you can start the recovery process.