I'm sorry. I was reading a bunch of things quickly and mixed your issue with another one
.
Which version of KO are you using?
If you're pushing books using wireless transfer of calibre these books should receive their green tick after transfer them. If you're pushing books using a usb cable the same should happen.
If you keep your books in a folder other than platform defaults (/mnt/onboard for kobos) and connect to calibre wirelessly only the books there will be reported as in device.