Originally Posted by magphil
Any hint for :
1) Removing those 2 empty shelves
Would be welcome.
Calibre has a "remove empty shelves" options in the Kobo driver page. It might edit the kobo's onboard database for you. It's under "Preferences -> change calibre behaviour -> advanced -> plugins -> device interface plugins -> KoboTouch -> customise plugins -> delete empty bookshelves".
Next time you sideload something via Calibre, it should get rid of the empty shelf.