First, and most important of all, congratulations on not listening to the two vets who sound like blithering idiots IMHO.
Were any x-rays taken by either vet? Was there swelling, is that why the first vet first thought it was an abscess and then an inflamed joint? If he thought it was an inflamed joint, why put your cat on antibiotics rather than an anti-inflammatory? Did I.R. have a fever? As for feline AIDS, this is a very unfortunate term for FIV, and a true misnomer (except for it being an auto-immune disease.) The very great majority of cats with FIV live full, healthy and long lives. They are more prone to infections and take a little longer to get over them, more prone to stomatitis, and they seem to be more prone to cancer in their teens, but that's it.
As for the limping and then partial recover after more than a year, I have no idea. An MRI when she was ill might have shown something. I have a foster cat called Challenge, only three years old , and I also thought his limping came from a mild sprain until it went on for weeks. X-rays were taken and nothing was seen. He was seen by three vets who said the only way we might know the true problem was through an MRI - which the shelter can't possibly afford. We've tried Cosequin which helped for a few months and then stopped. Now we are trying very low dose of Prednisilone. However, he has been nothing like as sick as I.R., it's just that sometimes he limps really badly and holds his leg up because he can't bear to put it to the ground and other times he acts as though he's never limped.
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