Clearing User Applications Is Simple
The 1756-L1, -L55, and -L6x/A controllers you just remove the battery and power down the controller. If there's a nonvolatile memory module or CompactFlash card, remove that too.
The 1756-L6x controllers save the program to NVRAM even without the battery... I think you would have to just download a new program over the old one. I haven't had to clear the program on an -L6x/B yet; I just download my new program.
In every case, simply downloading a default program into the controller is the foolproof mechanism. There's no way that I know about to prevent that.