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The proof of Isabella being a Miller can be found in the two will abstracts below (these abstracts were made from the original records in York Co.):
The Will of James Miller Made: 29 Mar 1678. Proved: 14 Apr 1678. York Co., VA.
The Will of James Miller Made: 6 May 1656. Proved: 24 Jan 1656/57 York Co., VA.
From this we can see that Isabella was the sister of James Miller (d. 1678) and the daughter of another James Miller (d. 1657). I suspect that the whole Warner theory was aroused by the fact that she had a brother, Augustine Miller.