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While it's quite an interesting debate as to how foot- and endnotes can best be utilized in ebooks, I'd also like to try to help the original poster. The initial issue raised is the following:
In the conversion from WORD to EPUB, the numbering option setting (number footnotes consecutively through the document vs. restart numbering for each section) is being ignored -- see attached.
OBSERVED BEHAVIOR: Regardless of the document setting, numbering proceeds consecutively through the entire book.
DESIRED BEHAVIOR: Numbering follows source document preference.
The poster also mentioned that the wordtoepub tool does preserve numbering preferences properly, which suggests that the relevant information is present in the source file.
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