Originally Posted by st_albert
Late to the party, as usual, but I thought I'd comment that it has been our experience that no matter how many rounds of substantive edits, copy edits, and author proofreads are done, many typos (and in extreme cases, stylistic changes) are only caught in the printed proof.
Therefore, we usually defer the production epub version until after the "final" corrections are made in the InDesign master file.
ID -> epub export is fairly straightforward even though we're still using CS4, especially since the vast majority of our titles are fiction; so there are generally few internal illustrations, tables, formulae, etc. to fuss with. Strict use of InDesign styles (a collection of which, stored in a template file, constitutes our nearly-universal house style) and an absolute ban on local formatting keeps the generated epub stylesheet managably simple.
The final touches are then made in Sigil, and another epub is made with modifications suitable for kindlegen conversion to mobi/kf8.
This is almost exactly what we do when we have a POD Package (print, epub and mobi) ordered, although we are not
primarily a print shop at all. We added print layout (essentially, for fiction-style layout or memoirs only) as a client accommodation, humorously enough. But this is how we work as well, when we have print. We do, however, have about half of our print clients come to us after they've pubbed their ebooks, and from that point we extract the html and work backwards, essentially.
For us, whether it's an e-job or print, do exactly what you do: make the final touches in Sigil, and make a dupe ePUB with mods for KindleGen conversion. On some
books, we don't need to mod the book for KindleGen, but most need some minor tweakage.