Thank you all for your input! It just seems like a natural thing to expand the information of one particular book by the comments and highlights added to it. The way it seems to be now is like iPhoto: You edit pictures, but only in a virtual realm that has nothing to do with the actual files on your hard disk. So when you send the file to someone, all the annotations stay behind. A bit like a librarian's dream.
Ok, I guess I have to live with what I have and just stick to one ecosystem.
Thanks again.