Best way to keep story synchronized across formats in InDesign?

I am working on an ebook that will be published as pdf and epub, and possibly another format, and all of the work is being done in InDesign CS4 (though I plan to use Acrobat for the final PDF stages.) My problem is how to work with the stories when I'm trying to prepare them for two different formats. The stories are basically done and I've split them into duplicate sets to prepare each set for its own format, but there's the danger of making small edits here and there and ending up with two substantially different versions of the same book. The PDF has a lot more formatting, of course, and some of the epub titles and styles have changed to control the look of the table of contents.
Should I keep one set of stories and copy them to separate versions for epub and pdf when I'm actually ready to publish, work towards one format and export the stories to new files when I'm done with the first format and ready to work with the second, or work with conditional formatting, or....?
Any suggestions? I figure this is what InDesign is for, but I can't seem to find a best practice for this scenario.

Best practice is to keep one single file as long as humanly possible.
In this case, you "branched" a version for another format; I'd suggest you don't edit that any further (apart from the formatting stuff you mentioned), but inform your client this version is to be worked on. Work on your "real" version until it's really really done, and only then make other versions.
It's a different story (no pun intended) if the transition between the two versions can be automated; that way you'd still only work on the 'real' version, but then you could generate the other with every edit you make -- you should still not be doing any work in the dumbed-down version.

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