I had a long discussion with an AME about this as my wife has SLE. Her medical lapsed when she was pregnant and her diagnosis was subsequent to this. His view was that it could go either way but that if you held or had held a medical it would be harder for the CAA to revoke or refuse it than if you were applying fresh. SLE can vary in its severity. My wife was very seriously ill at one point with multi organ problems and cerebral lupus. She also has "sticky blood". At the time the diagnosis was poor but she recovered and for some years now has virtually no active symptoms and has a very low maintenance dosage drugs. The problem you may experience with regard to a medical certificate is that the blood problem can effect blood pressure and increases the risk of stroke although this can all be ttreated with medication.
Good luck