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Hmm, my method would be creating a single HTML file via Sigil, extract all the files and open the HTML in Word. Perhaps Calibre is doing something strange to the links.
I cannot imagine the Amber program has added value, they almost never have. Most of those kind of programs use the same conversion routines as Calibre.
I actually started thinking about this recently. My biggest worry was the retaining of styles, hadn't thought about the footnotes yet.
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