@FoolForBooks, @andrys: I've revised the first posting to help users who have not yet migrated book management to calibre with the process. I made some changes to the Save books functionality which won't be available until 0.6.45. With those changes, it is possible (though somewhat tedious) to migrate books and annotations from the native Kindle-style storage to calibre-style storage.
After the architectural changes are in place for the device drivers, it should be simpler for new users to migrate annotations with their books.
Thanks for the feedback.