As jonathanm says probably better to do a manual backup of a known good configuration. A cron job would not take care of everything anyway because:
.key file is tied to a specific flash drive so mirroring that is pointless. You could just have a second .key on the other drive though.
super.dat has the current state of the array so if you copy that while the array is started and then boot using that copy unRAID will think it had an unclean shutdown and will start a parity check.
The flash volume unRAID boots from must be named UNRAID, so if you had two flash drives one of these would have to have a different name and would have to be renamed before it could be used. Not a big deal but something to be aware of if you try to have two of these installed at the same time.
Simplest is just to copy the flash to another computer anytime you make any changes. You can do this with the array still running if you share the flash drive. Just be aware of that point I made above about super.dat.
You don't need to copy super.dat unless you actually make some change to the array, such as adding, changing, or removing a disk. I think you can still get to the flash share if you stop the array, so maybe just stop the array after you get the "new" array configuration fully working again, and copy super.dat then.