Hi, Jack.
Actually, the solution to your problem is easy: don't use separate INDDs. It's easy to create fixed-layout ebooks, with the required separate XHTML files, from one or several INDDs. Bob's right:
"Creating Fixed-Layout eBooks, ePublishing with InDesign" http://amzn.to/WBjwz1 will explain just how to do all that. It's about creating fixed-layout ebooks from within InDesign, just like my ePublishing with InDesign CS6 (http://abbrv.it/DigiPubID) is about creating all sorts of digital publications from within InDesign.
