I'm looking for a description of how an EMP might affect a magnetic levitation train system that is NOT connected to the local power grid. Specifically, if the maglev was active, would the train be thrown off the tracks and rendered unusable, or otherwise disabled, or would it simply suffer a loss of power and then be able to reboot and run perfectly fine again?
To my understanding, a maglev train is propelled by magnets above and below the rails, that pulse in precise timing to send it forwards (or to slow it down when it needs to stop). These are also responsible for the levitation effect: the magnets hold the train a small distance above/away from the rails.
If your EMP pulse managed to kill the power to the magnets, the probable result would be the train dropping a few inches or so onto the rails and grinding along until it lost its momentum. Going at several hundred miles per hour, this would be dangerous in the extreme, but with such a tiny drop I don't think it would run off the rails unless there was a sharp turn (unlikely, given that you need to consider the G-forces on passengers when the train is operating normally) or the rails were unable to take the train's weight (which undoubtedly would be a building code violation).
This would terrify any passengers, beyond all doubt, and the resulting damage to the magnets would most likely render rails and train all unusable without expensive repairs, but I doubt you would have any casualties. Unless, of course, the timing is unfortunate enough to catch a train as it's about to slow down to enter a station, with another train on the same track at the other end of the station loading up with passengers.....
I think one might design a maglev train with induction braking that would be robust enough to use the kinetic energy of the train and permanent magnets to not only stop, but also maintain the maglev effect while the train was moving. The train would still ultimately drop onto the rails, but not until it spent its kinetic energy braking / floating.
Induction brakes are already used on some maglev trains.
The simplest linear, eddy-current brakes have two components, one of which is stationary while the other moves past it in a straight line. In a rollercoaster ride, you might have a series of powerful, permanent magnets permanently mounted at the end of the track, which produce eddy currents in pieces of metal mounted on the side of the cars as they whistle past. The cars move freely along the track until they reach the very end of the ride, where the magnets meet the metal and the brakes kick in.
This kind of approach is no use for a conventional train, because the brakes might need to be applied at any point on the track. That means the magnets have to be built into the structure that carries the train's wheels (known as the bogies) and they have to be the kind of magnets you can switch on and off (electromagnets, in other words). Typically, the electromagnets move a little less than 1cm (less than 0.5 in) from the rail and, when activated, slow the train by creating eddy currents (and generating heat) inside the rail itself. It's a basic law of electromagnetism that you can only generate a current when you actually move a conductor through a magnetic field (not when the conductor is stationary); it follows that you can use an eddy current brake to stop a train, but not to hold it stationary once it's stopped (on something like an incline). For that reason, vehicles with eddy current brakes need conventional brakes as well.
I could not find specific diagrams of how the induction brakes on maglev trains work. If I were designing them I would have permanent magnets on a deadman switch swing out when the power went and then produce eddy currents to slow the train.
Frictional losses by the train falling onto the rails and "grinding along" (to quote @Pallaran) would make the emergency induction brakes kind of pointless. There has to be something to prevent this grinding. The cheapest way would be friction pads like brake pads on the grind points. But if you are using permanent magnets for emergency induction brakes you can use the same principle and use permanent magnets for emergency induction levitation, or electrodynamic suspension.
If there are permanent magnets on a deadman switch ready to tap the trains own kinetic energy and turn it into levitation and braking, the EMP-fried train would coast and brake until its kinetic energy was gone.
It was frustrating not being able to find a schematic of how real maglev trains accomplish these ends. Probably it is proprietary.
I envision a scenario where the heroes deactivate the brakes and trigger the Atlas rocket being carried on this train, the rocket exhaust now providing impetus and the emergency induction levitation turning back on when the train got up to speed.
EMP's generally will disable or outright destroy any complex electronics inside their effected radius. Maglev trains are levitated using electromagnets, so the moment the EMP hit the track, the train would fall onto the track. If the train were stationary, this wouldn't be too bad, but if it were traveling at full speed, with some reaching speeds of up to 375 mph, this would be disastrous. The train would act just as if it were a traditional train running off of its rails, only at a much higher speed.
There are some protections in place, and electromagnetic suspension (EMS) systems are designed to run temporarily in the case of a power failure, but these systems generally only run for a short period. Additionally, the systems to monitor and activate these emergency measures would more than likely be fried in the EMP itself.
As for EMP shielding, perhaps one could shield the controls themselves, but I am unsure if you could shield the electromagnets themselves, simply due to their location and function.
In the end it comes down to how paranoid the owners of this maglev system are. If they believe that an EMP threat is viable, then perhaps they will shield the emergency systems, thus allowing the train to have a chance to save itself in such a scenario. If they aren't as worried, then it will in all likelihood end in a catastrophic failure.
Note: This answer is based on my own understanding of EMP's mixed with a small amount of research I did into maglev trains while writing this, so if something I said sounds suspect to you, I encourage you to research it for yourself.
Maglev trains are designed with multiple levels of redundancy so that catastrophic failure is exceedingly unlikely (or rather that it is an acceptable risk), if however your EMP managed to shut off all its power and fry all its redundant systems, the train (because of conservation of momentum) would indeed fly off the tracks at high speed likely killing everybody aboard and destroying itself in the process.