Did you ever resolve this?
I suspect the problem is related to the new ability of ID to have multiple page sizes. You can apply a master to apage, then cvhange the page size without affecting the master, and apply a different master without changing the edited size.
No, Peter, I never solved it. But thank you for asking!
I finally started a whole new book, with the smaller master pages. I saved a few blank pages for each chapter file, then I copied and pasted the text of each chapter onto the new pages. Fortunately I was able to transfer paragraph and character styles to the new document, and the formatting of the copied text transferred also.
But it was still a lot of work.
I don't even want to think about trying to design a document with different size pages!
When I've had to change the page size for a book like this I've done it using Layout Adjustment and Document Setup, then making whatever changes need to be made to masters, but the last time that was necessary was in CS4, so I don't really know what would happen in later versions. I do think that if you changed the document setup size first, then synching the masters would probably have worked (though you might alos have to turn on Layout Adjustment, too, depending on whether there were master text frames or not).
I've lost track of all the different approaches I took! I may not have done them in the right order, though. I did learn one thing: don't do that again!
If I'm ever crazy enough to get into this predicament again, I'll probably do as I did on this one: set up a whole new book with clean formatting.