I have accidentally removed the center rail while working on Atlas track. It is easy to do. Removing the center rail leaves a mold mark down the center of the ties. You might be able to cover it with ballast but this may be hard depending on the look that you want.
The switches are wired for 3-rail which means that both outside rails are connected. They will short in 2-rail operation unless you isolate the outside rails. This won't matter if you only use battery power. 2-rail conventional or DCC will be a problem.
I have had problems running 2-rail equipment through O-72 switches because they are too sharp for anything but short cars and engines. You do need to modify the guard rails as mentioned above. I wouldn't attempt any 2-rail equipment with any curve smaller than O-72. Scale passenger cars with 2-rail wheels are an issue but can be modified to work on sharp curves. I think the smallest Atlas switch size you should use for 2-rail equipment is a #5.
I think that you would be better off selling your gobs of 3-rail Atlas and using the money to buy 2-rail Atlas if your goal is to run 2-rail battery or DCC. NH Joe
