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Any TOC you see at the beginning of the pdf would be a side effect of the original pdf's inline/user visible TOC. As far as Calibre is concerned that TOC is just a bunch of text indistinguishable from any other text in the book. So it just leaves it in place. While it's easy for a human to see and fix that problem, creating a heuristic for a machine to accurately guess where that text is would be quite difficult.
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