What you are seeing is expected. Books sent to your Kobo will not show as on device until after they are imported to the Kobo's database. Since quitting calibre and then restarting calibre does not import the books, they are not present in the Kobo database and will not show as on-device.
Since I have my on-device books shared between Nickel, KOReader and Plato, I send the books, safely eject to import the books to the Kobo database and then reconnect to update metadata. This also allows me to use KOReader's search of the calibre.metadata file to work.
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