(from WIKI)
The E-4B is designed to survive an EMP with systems intact...
With in-flight aerial refueling it is capable of remaining airborne for a considerable period, limited only by consumption of the engines’ lubricants.
Aircraft are natural Faraday shields. An EMP is basically like a lightning strike, there is nothing magical about the properties of an electro magnetic pulse. There may be some temporary disruptions, but aircraft will not start falling from the sky...Google..not sure if correct