Just that I got it right - you are trying to sync the same USB device from 2 different rekordbox machine with different Playlists or are the 2 rekordbox DBs are the same and in complete sync?
I think when syncing a rekordbox USB with a different PC the previous DB on the USB stick gets replaced with the new one.
Once the new DB might not include all tracks on the USB stick, the tracks might be still on the USB but not part of the rekordbox DB and therefore not visible on the RX.
Have you checked the Folder view to see if the missing tracks are visible there?