Eheh this is the hilarious part... I had to reset my kobo few weeks ago and I forgot to reinstall my backup script
Luckily I was able to extract the Bookmarks table, that is the most important thing for me (by the way, I think I'll add an option to backup only that table. For me is enough).
Yes, calibre did not report any error. But I noticed the corruption when I rebooted the device, not when I disconnected it. This is why I supposed it's nickel itself. Or maybe a coincidence.
Next time I'll backup the database before any calibre operation. If a corruption happens, I'll reboot calibre in debug mode and I'll redo the operations.