Some doctors stop taking an ANA test once it come back positive for the exact reason that you are talking about. ANA's change in most of us. They can be worse when in a flare and they can get better because we are feeling better or because our meds are working. One thing that is not understood by many people is that lupus symptoms are cumulative, meaning that they add on top of each other. You don't have to have your symptoms at one time you just have to have enough, over time, to get a diagnosis.
So, the ANA thing is normal. I wouldn't even pay any attention to the results from now on. Once it has been there it really tells you nothing