I had exactly the same problem in CS4, which is why I switched to CS5.5 -- but apparently nothing has changed.
I have a book of about 30 chapters. It was originally set up in 6x9 format, but after it was all formatted, my client decided he wanted the pages 5x8.
It should be easy, right? Just change the layout for the master pages of the Style Source document, fix the text sizing, etc. Then in each ensuing chapter, just download the new masters from the style source document. When I get a warning asking me if the master pages in the target document should be overwritten, I say yes and it does its thing.
Only it doesn't work. Oh, the text in the masters is all over the place, which is to be expected -- but the master pages and the book pages are still 6x9, not 5x8.
I tried synchronizing the book, being careful that Master Pages is checked in the options. I got a warning that some of the text would need to be fixed. No problem. Except that the pages in all the documents except the Style Source are still 6x9!!
I have a feeling I've wasted my money on the upgrade. A lot of bells and whistles have been added, but the CS4 problems aren't solved.
Please, can somebody help? I do this for a living, and I'm wasting waaaaaay too much time trying to clean up messes like these.