Well, I tried a few rough tests converting epub --> epub with Calibre. First attempt was different, but just as mangled as the Sigil output. But now I see the problem.
In both Sigil and Calibre, I see that I cannot start renumbering footnotes with #01 on each chapter. I will have to start with 1 and number straight through to 45. Then, it keeps the anchors attached to the correct splits/chapters.
I think I was expecting a miracle from the software. (hey, a person can dream, can't they?)
Thanks to all for your help. eschwartz, your Calibre tip helped lift the curtain of confusion.
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