If an autoimmune disease is in remission at the time of ana testing could the test be negative but possibly still have the disease. eg ra or sle ?

Yes: Autoantibody tests can sometimes become negative when the disease is in remission. However, the high likelihood is that the underlying disease is still present.

Yes: The anti-nuclear antibody (ANA) titer fluctuates over time, and it's also a test fraught with pitfalls within the lab, with results hard to reproduce even from day to day. I'm very glad you asked; this is a thoughtful and important question that touches on how tricky it is to manage these diseases. The key is treat the person, not the lab value.