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OK, let's try to take a logical approach to this:
1. Books are inside the "documents" folder on the USB drive. If they're there, they show up on the device. If the directory is empty, then nothing will show up on the Kindle.
2. You say that your device is in airplane mode all the time, so it's impossible that files are automagically synced from the network.
3. You say that you deleted the files on the USB drive.
4. And yet, somehow these files mysteriously re-appear on the Kindle.
Conclusion: there are exactly three possibilities: a) the files weren't really deleted in the first place, or b) they were, but some process on your Windows box keeps putting them back. c) would be that your Kindle has super powers and can create meaningful content out of thin air.
Concerning a): make sure that the files are actually deleted. I believe using Shift+delete will irrevocably delete files (as opposed to just putting them to Trash) on Windows ("I believe" because I don't do Windows). Just in case: make sure that you properly safely eject the drive - don't just pull the cable!
Concerning b): make sure that you're not running some funky software which would be doing such things. What comes to mind is some automated backup solution or something running havoc.
Concerning c): patent it and make billions.
Finally, you could try to re-format the USB partition. Maybe it's corrupted (which might explain such weird behavior).
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