I can't give any better advise than what SleepyInSeattle has given you. I just want to reiterate that you must take control of your health care. You know it is not in your head and your symptoms are real.
Ask your rheumy to order a 24 hour urine test (if that has not already been done) to determine if, in fact, there is evidence of damage to the kidneys. With reference to your flare up, may times doctors will direct you to up your dosage of Prednisone to get you through the flare, then slowly reduce your dosage back down to a maintenance dose. You might want to ask about that possiblity.
I don't know how long you've been on Plaquenil, but as Sleepy mentioned, it can take up to six months or more before you see any significant results as it is a cumulative medication and must build up in your system.
Has your rheumy made any follow up appointments with you? If so, when is your next appointment? Whenever that is, do take Sleepy's advice and inform him of the PA's statements. Also, between now and then, keep a detailed journal of your symptoms, your meds, when your symptoms are worse, what you feel like when they worsen, how long it lasts, when you feel better, what your activities were when you feel worse and when you feel better. DO NOT let any doctor brush you off (that includes PAs). Learn as much as you can about the disease, its medications, its treatments and how it affects you. In this way, you can have informed conversations with your health care team and you can work with them to make knowledgable decisions about your health care.
I wish you the best and let us know how you are doing. Whatever you do, do not give up!
Peace and Blessings
Look For The Good and Praise It!