After a brainstorming session I have an idea... portable drive snapshots
Obviously what I'm about to suggest could be handled by a separate app and perhaps that's the way to go ultimately... but in my mind this should be integrated into or at least an addon for the portableapps.com platform itself.
So what am I talking about? Well... snapshots combined with an auto-revert feature. A way to revert any external changes to the files on the portable drive automatically.
Why?