I have postural orthostatic tachycardia syndrome and lupus- does that mean the lupus has already attacked my brain with neurologic issues?! poor prognosis?

POTS not specific. Those are some very tough diagnoses. Pots has several types and is usually related to an issue with nerves or hormones rather than a brain lesion -- it is not a condition specific to lupus. The way to evaluate for brain lesions is through neuroimaging. In your case, i very much recommend having an in depth conversation with the physician(s) familiar with your specific case.
It does not mean .. No it doesn't mean that at all. Their are many ways to assess disease activity in lupus and/or lupus cerebritis. Postural hypotension is not a feature of lupus cerebritis. Talk to a rheumatologist about your concerns!