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

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!

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.