I had no problem whatever cleaning up a 140,000-word non-fiction books with a few hundred endnotes. Word's endnotes did need a bit of massaging before they looked professional. Like so much in Word, it handles notes in a fashion acceptable maybe in an office environment, but not in publishing.
Indeed, it was simple enough that I don't really remember the process, except that it took me three passes to get the entire book shaped up in Sigil. The problem AFAI recall was Word's inability to display word count and spellcheck on a file so large.
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