Calibre support for Kobo Annotations
As of Calibre 0.8.24 later this week (normally Friday) the Kobo driver has been updated to support importing annotations from the device.
The annotations import and are inserted into the comments area of each book. Note that the book in the library must match a book on the device for the annotations to be retrieved. That is, if the book is not in your library it will not retrieve the annotations from the device copy of the book.
Which brings up another recent feature. It is possible as of 0.8.23 to add kepubs to your library from the device. They are still encrypted so are pretty much useless but you can update the cover, metadata and use them to retrieve the annotations.
To retrieve annotations, right click the send to device button and choose fetch annotations.
It seems to work well with and without sdcards and with epubs and kepubs. No doubt there will be a few issues in the first go around.