How frightening! Yes, lupus can affect the brain - usually the brain fog many of us talk about. Your stress level - and lack of sleep - are certainly playing a part as well.
At one point I was having some issues - mainly fog and (for lack of better way to put it) missing words. I was having trouble getting out what I wanted to say. I had an MRI, EEG and a full neurological workup. Turns out I did have some "lesions" in my brain, but they haven't caused me trouble since. I think part of it is knowing - I know there will be times I'm unsure of words, I know there will be times I'm foggy. But I also know that if I get the rest I need and manage stress (if only by taking a deep breath before I start opening the mouth...) I do OK (mostly).
I'd encourage you to talk to your rheumy, possibly ask for a consult with a neurologist.
I hope Saysusie will jump in on your post, you need more information than I can give you!
Many hugs and much encoragement...