I remember now: given that Word clusters the endnotes in a single file, I just separated it out, cleaned it up myself, and added it to the end of the book.
I also moved the return-to links a bit earlier, either to the beginning of the paragraph or anyhow the beginning of a sentence, since otherwise the ebook return (Kindle, anyhow) is simply to the actual footnote number, which regularly orphans (widows?) a single word at the top of a "page".
There were a lot of photos and maps in that book, which maybe bogged Word down. Or perhaps it was the limitations of my then-computer.
Anyhow, no problem with using Word2CleanHtml dot Com on a book with endnotes if you're willing to mess about with the html a little bit. (And if you're not willing to do that, I'm not sure I'd recommend Sigil at all, and certainly not for a first book.)
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