Sure … you can do it completely manually, or you can save some time if you have CS4 by using the Move Pages command. Create starting INDD files first w/the right page dimensions, one per chapter, and open them. Then select a chapter's worth of pages you want to move in the Pages panel and have Move Pages move them “At Start of Document” to the appropriate chapter doc. Rinse and repeat for each chapter.
Make sure though that your text frames are completely self-contained within each chapter before you move them. There are some scripts that can help you with that if that's not the case.
AM