I do all substantive and copy editing in Word, and convert from DOCX to EPUB.
I use the epub editors (the one in calibre and Sigil) to do any necessary markup related editing - which is not often needed. I use the various checking tools they provide, scan the word list and Sigil Reports for any glaring anomalies, and do quick looksee's in ADE and calibre viewer.
The 'books' I'm referring to are not commercial books, they are official papers, think tank reports, media transcripts, learned journal articles, dissertations - typically 10-60K words.
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