Kobo don't have a way to save the annotations somewhere else. There are other ways to do it. Which is best depends on what you want.
Firstly, the firmware stores the annotations in the internal database. This is an SQLite database and the table is called "Bookmark". For purchased kepubs, Kobo syncs this with their server. Then it is synced back to other devices or the desktop app. For epubs and PDF stored in the main memory of the device, the annotations are also stored in a file. These are under the directory "Digital Editions\Annotations". The files have the extensions "ANNOT" and contain XML. All of the methods read the database. But, you can also look at the file if there is one for the book.
The methods I can think of are:
- Calibre has a "Fetch annotations" option. This copies the annotations for all books to the comments field of the book in the calibre library. The annotation is appended to whatever is already in the comments field.
- My Kobo Utilises plugin can display the annotations for the selected books in a window. It also has an option to backup the annotations files.
- MR user tshering has published a Windows tool that will display the annotations. A search here should find it.
- There have been some other scripts published to copy the annotations out to text files. Again, searching here should find them.
- Recent firmware have a hidden option to display a menu option to export the annotations for a book. The menu options is on the books menu in the library. It creates a text file with all the annotations for the book in the root directory of the device. To activate this, the following lines need to be in your "Kobo eReader.conf":
There might be some other methods, but I can't think of them at the moment.