Rails has clever systems for locating trains by detecting circuit shorted by trains' wheels, no need to replace that with GPS. Besides railroads passes valleys and tunnels, GPS won't work anyway.
The absolute last resort for trains is semaphores and mutexes based on physical tokens. Those concepts came from there, and were still used sometimes to this day. Doesn't sound high tech, but it works.
They should have lots and lots of local transmitters.