Thank you meeera to be interested in my case
I use the option in calibre, to disconnect properly (the disconnect submenu of my advice).
To give you an example, the last time I used Calibre was to add 2 fanfics and a book. After disconnecting, the update on the kobo stopped at 6%. I have waited for about 4 or 5 minutes and then I have decided to switch it off.
The part when you talk about signing out and disconnecting, I don't clearly anderstand (sorry for my english).
But what I can say is that I go to parameters/account/disconnect.
Then my kobo restarts and it asks me again my kobo account, and then sync and rebuild the database.
I have already tried to sign in a new account at kobo.com when I met my problems about persistents empty shelves, but it changed nothing.