Perhaps furture versions of Calibre will support shelves? Well, we could always hope.

Until then, you can try backing up the file .kobo/KoboReader.sqlite. This is where the list of shelves and content of each shelf is stored. You will have to restore your books to the same filenames and directories though, since the database tables refer to the files by name. I also don't know if this data is preserved while rebuilding the database.

Incidentally, I noticed a new table called ratings. I wonder if this is foreshadowing a future feature.