I suspect there is something wrong with the database on the device, but I would have expected calibre to report an error when you connected it. But, my Kobo utilities plugin has a function to check the database. That does a complete check and will report any errors.
If there are any database errors, the fix is to sign out of the Kobo account on the device and then back in. The will generate a fresh database and reload any books on the device.
If the database is OK, try powering off and on. This will restart the software and force a reread of the database. That should also get it to recognise the card isn't there.
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