If you use RailClone Tools then the RailClone object is used to generate instances and then turned off. It is not permanently replaced. This means that if you want to go back and make changes you can use RailClone Tools to delete the instances and re-enable the RailClone object to continue editing. When your done just regenerate the instances again before rendering.
Unfortunately this is a limitation in the way V-Ray handles the RailClone object. Are you able to use a Material ID pass instead?