A shutdown caused by EMP is the work of a protective system and had to be installed in anticipation of an EMP event.
Otherwise EMP just permanently fries circuits if we are talking electronics, and with fine metal mechanical parts welds them together or burns them apart like a light bulb filament.
OTOH whatever it is that the Mad Boys use instead of electronics could use completely different principles, so much so that it might actually be able to rebuild a disabled system automatically, or the observed field effect only temporarily affects the Mad Science Motivator Fluid.
In other words, all bets are off.