Well... two weeks changes everything. Miss came good again. I stopped giving her grain when I gave up on her [she was still on pasture and had free choice hay] and she came sound.
Feels like a bad dream now. She hasn't taken one single lame step in 9 days, which is a record for her. She actually PUT ON weight, and her coat has a much better shine to it.
All signs point to her lameness being because of her grain intolerance [hindgut acidosis can cause hind end lameness]... I don't doubt there was an injury or something at some stage which spurred my vet to think it was more serious but the ongoing lameness was in the absence of any heat or swelling, and is now gone completely. I am therefore doing the same things I would do with any 2yo TB with her, pushing my luck regarding her soundness, because I don't want to have her sound for 6 months or a year and then have her break down again the moment I start to break her.
I took her on intending that I would have a trainer break her for me, but that I would do as much as possible myself, and if I felt like I was in over my head I would get help. I did get in over my head with some of the groundwork, but I got help, and she's a totally different horse to the one she used to be.