I had a communication error with my Kobo Clara during connection with calibre. I did a safe eject and reconnected.
No problems thereafter, only that calibre now reported no ebooks "on device" anymore, which is strange.
DB checks on calibre and Kobo did not reported any problems whatsoever, while Kobo reported, showed and accessed all previous loaded ebooks, and calibre insisted they were not (found) on the device.
I could add new ebooks, which showed up on the Clara, and calibre marked these as "on device" as expected.
As a check I did let calibre rediscover all ebooks on Kobo, by renaming the "metadata.calibre" file so it was rebuild. But calibre still insisted there were no ebooks on the Kobo.
I solved it by removing all ebooks on the Clara, rentered them via calibre, and the Clara and calibre were in sync again with all the newly added ebooks shown as "on device".
For the moment I'm fine, but is there a better solution to solve this kind of situation might it happen again in the near future?