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Is there a method of importing a PDF with TOC and bookmarks ect.. into Abbyy than export directly to MOBI with format, headers and footers intact? I've found that Calibre is a great ebook manager, but a terrible encoder. Abbyy Finereader seems to have better encoding capabilities than Calibre and Writer2ePub.
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The problem is the PDF format, not calibre or Writer2ePub. PDF should be considered a final destination for a document. Any method of converting PDF to MOBI/ePub etc, is going to involve a lot of manual cleanup of the formatting. Nature of the beast. You'd be better off sizing/cropping the PDF for your tablet's screen size and reading it that way. This type of conversion will always be problematic.