S.J.
I don't think you're ovary went away, it probably shifted underneath another organ. I have had a ton of ultrasounds...and many professionals are not very good at doing them or reading them. It's possible that you do have another cyst which is causing pressure on a nerve and that's why you have leg pain. I had leg pain with uterine fibroids which I had removed.
As far as what to do, cysts usually go away on their own, but they can get really big requiring surgery. It's good you are seeing a specialist...hopefully an obgyn.
The only other thing that might be going on is a torsion, This is where the ovary or supporting structures twist causing pain. It really is something that a doctor should look at.