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Are you disconnecting your Kobo and allowing it to import the books before restarting calibre? When you first connect to calibre, the books shown are those imported to the database which is done when your Kobo is safely ejected from the computer. If you are seeing the Importing screen on your Kobo, the first thing that pops to mind is that you have a corrupted database.
My suggestion would be to sign out of your account (Settings => Account => Sign out ). This will replace the database with a blank copy and then re-import any sideloaded books.
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