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For me, the simple way is to finish up the book in Word, convert the footnotes to endnotes (it's a one-click process), and then clean up the html before opening it in Sigil. Word does a splendid job with this particular task.
I do however generally move the anchor back to the beginning of the paragraph or anyhow the sentence, because Kindle especially has a tendency to return the reader simply to the footnote number, which hangs disconcertingly at the top left of the screen. If the endnote is at all lengthy or interesting, the reader might well have forgetten the context.
I also get rid of the superscript, instead enclosing the number in square brackets for visibility. Superscripts irritatingly increase the spacing between the line they're on and the line above, which to me looks sloppy.
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