I may well, but the title indicates that it is more about creating ebooks (I couldn't check the contents) than about Indesign's functionality. If there is a specific point in the book that solves this issue, I would be more than happy to purchase it. Does it? As my question really relates to Indesign's operation, I'm really hoping that someone with a far better knowledge of the program than I will help shed some light on the problem.
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.