There are two ways to get a book from the device into calibre.
In both cases, first connect CC as a wireless device and select the device view.
- Method 1: right-click on the book and select "add book to library". Downside: the book is added as a new book unless the book merging options prevent that.
- Method 2: right-click on the book and select "save to disk". Put the book somewhere it will be easy to find. Switch to the library view, select the book, press E to edit metadata, press the "add format" icon (a book with a plus sign on it), navigate to where you saved the book, select it, and press OK. This will replace the copy in your library with the copy from your device.
Note that unless the annotations are stored in the book itself, neither method will solve your problem.