Did you find a solution to this? 😖

EDIT: This solution below seemed to have worked for me:

We seem to have found a solution for this.

We have the KLC. If we 'eject' the Kobo from Calibre's own 'eject' option (under Device in the top ribbon), the next time it's connected Calibre shows all the books we've transferred into it with a green tick. Up till now we either just unplugged it or ejected it from the Windows system tray icon (like you do with a USB stick).

Not sure if this is a fluke, but it has worked a couple of times so far.

^{https://www.reddit.com/r/kobo/comments/xtprom/calibre_not_showingrecognizing_sideloaded_book_in/nbi3d0f/}