Currently, there is only one set of intersect markers for getting close to a target for, say, docking, and manoever nodes change that set. This is annoying, as when you get rid of that node they could change a great deal to reflect what has actually gone on, not what the manoever would have done. Adding a second set of markers, to show what is actually happening (like what we have with orbits, the manoever displays a predicted encounter with Minmus but your actual orbit is still shown orbiting at 100km above Kerbin), would solve the problem.