In NYC, subway repairs are performed while the system is active. Crews haul sections of track down the tunnels, walking next to the third rail, while a worker stands a few hundred feet behind or ahead (depending on the direction of the trains) with a colored light, to indicate their presence, and serve as an early warning to jump aside. These crews have been mowed down when the train came in the wrong direction and there wasn't an early warning (these guys have a proper title, just don't remember what it is) guy facing that way.
The point being. I don't know.
Watch out for the third rail. Most tracks have some sort of a walkway on the side, so use it if available. Don't expect a train to stop in time if you fuck up (and if it does, expect jail time if you're caught down there). If the worst happens, remember that there may be just enough space below the train if you lay flat and suck up your belly (still keeping from the third rail).
On one hand, you could try and see what kind of reflective coats/vests the crews in your area wear. That would marginally improve your safety and greatly improve your chance of being caught. Probably better to have dark (but not black) clothes that you can blend in the darkness if a train comes.
Also, I'm sure your abandoned stations don't have much security, but what about the live ones? Is the station manager going to see you (on camera, perhaps?) sneaking down into the tunnel? Or have you planned a different point of entry?
