It is my understanding that autoanitbodies do go away when your disease is in remission. Most of us with an AI disease will initially test positive and then go into remission. I have not tested positive for any of the 3 diseases (lupus, scleroderma and polymyositis) that I have. However, I still have symptoms of raynauds which often presents with lupus, scleroderma and PM. None of my tests for the past 4 years have been positive. That does not mean there might be other autoantibodies that are produced by my diseases but are not tested.
MCTD (lupus, scleroderma, polymyositis). Diagnosed 2005. Kidney, liver, GI tract, dysphagia, raynauds, Barretts esophagus, quadriplegic in 2005. Recovered and now active in skiing, tai, chi, hiking, golf. Meds: prednisone 2.5mg, imuran 25mg, amlodipine, benazapril, omeprazole, potassium, folic acid, vitamins, maxide and various supplements and vitamins.
Remain optimistic and you can overcome the odds.