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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.
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