what do you mean, removed? blender doesn’t remove objects unless you tell it to do so. what could have happened is that your objects are being moved. why? this happens if more then one objects share the same IPO (curve data, hodling information about position, rotation and stuff). so if some of your objects appear in a different position after a render, select each of then and press “U”>> Object and Obdata. then reposition them and rerender.
it can’t be the normals, blender always renders objects (even if they are flipped)…
You’re using dupliverts to create the wooden supports and the ties… dupliverts that stem from the rail and the tunnel. That is your problem. The emitter never shows up.
For a quick fix that will keep you from having to change anything, simply duplicate the rail and the tunnel (shift+d) and then uncheck the dupliverts button on each.