I'm confused. Who said anything about trying to harden against EMP in software?

My understanding is that the real threat from EMP is physical destruction of the circuits by inducing voltages beyond what the wiring can handle. Any bit flips would be transient, since the EMP doesn't last very long (thus the P part).

Trying to use software to protect your chips from being fried by hundreds or thousands of volts being shoved through parts that weren't designed to handle it is clearly not viable.