She does not always mean good, and not always is she overt as to her real meaning.
I think "is" should come before "she" because of "not always". Is that correct?
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It is correct, if a little fancy/antiquated. Normally, in most common form this sentence would go:
She does not always mean good, and she is not always overt as to her real meaning.
Following a negating conjunction like that requires such inversion. Your case is unique in that the negating conjunction is spread between three words,
and not always and the spirit of this rule ceases to be as apparent, but take this:
She does not always mean good, nor is she overt as to her real meaning.
In this case the need for the reversal is obvious.