It is not uncommon for those with Lupus to have a false positive test for Lyme. Unfortunately, it does happen. In studies, a positive for Lyme disease was found in up to 40% of patients with established SLE and also in other rheumatic diseases. Lyme disease results from the spread of Borrelia burgdorferi bacteria living inside infected ticks. Lyme disease spreads only by a tick bite. Though the bite may go unnoticed, the infection usually starts with a painless, spreading rash where the tick had attached itself to the skin. So, unless there are indications (test results etc) and/or signs of the insect bite, the chances are pretty good that you do not have Lyme disease.
I am glad that your doctor is being thorough, but try not to worry too much about this.
Peace and Blessings
Look For The Good and Praise It!