Thanks for your help tshering, I now have a clean database.
But my problem is that my database corrupts as soon as I send a book with Calibre (even just one !), or when Calibre refresh the fields about shelves in the DB.
Here is the log, if it can helps :
Code:
calibre, version 2.22.0
ERROR: Error: Error communicating with device
database disk image is malformed
Traceback (most recent call last):
File "site-packages\calibre\gui2\device.py", line 87, in run
File "site-packages\calibre\gui2\device.py", line 503, in _books
File "site-packages\calibre\devices\kobo\driver.py", line 1787, in books
File "site-packages\calibre\devices\kobo\driver.py", line 1663, in get_bookshelvesforbook
DatabaseError: database disk image is malformed
The only way to get my kobo works, is to forget Calibre for now

and copy/paste my books, and use the auto shelves script...