I decided to have them moved out beyond the scope of the documents folder because it seemed like the simplest way to do it. This way, if something goes wrong you can always move them back manually, or at least you have access to the books through USB.
If someone has access to the USB partition on your kindle, no matter how you hide the books they will still be accessible. I aimed this script at "in-the-field" deployment, for switching profiles on the go.
I'm open to suggestions for doing this more efficiently, as this process does take about a minute each time.