Solved!
I have found a workaround with DB Browser for SQLite. First I copied all my books of my old Kobo in the same directory of my new one. Then I opened the bookmarks from the old KoboReader.Sqlite files, exported them in cvs and then imported them in the bookmarks of the new KoboReader.Sqlite. Apparently it works! I am so thrilled because the database thing was really puzzling me. Thanks geek1011 and DNSB for the hints!
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