SkyView doesn't really work the way you are thinking where you can just accidentally delete a file like you can on a PC.
There's no way to delete a file and make it not boot up, and the databases on the system aren't in "files" you can see. We've never once heard of someone booting up their SkyView and having their obstacle database somehow missing, so I don't see how having the database files is much help. SkyView isn't a Windows computer where applications are "installed" so there's no way or reason to re-install anything. If you call our tech support they will never tell you "try re-installing" something. Realize that if SkyView fails to boot, no files on the stick will help because you will have no way to install them.
If you really want to keep that data around, the data you want is the 4GB terrain data for your region, the latest software .DUP file, the latest aviation database, the latest obstacle database, and the latest sensor .SFG. The only time I can think this would be really helpful is if your screen died and you got a new screen, but all of those files can be downloaded off our website at any time.
The real file that can help you is keeping a safe copy of your "Settings export" .DFG, which would let you recover your settings easily if you ever needed to. That's the only file I keep around on my plane.