When did you first notice the line missing? Just after launch, after some staging during lanuch or on the way to the Mun? I think the important thing here will be learning what kinds of events can cause this.
I've got a similar problem here, I was doing an Apollo-style mission to the Mun and after undocking the lander from the orbiter, the lander didn't have a trajectory. Looking through the quicksaves it seems like it somehow switched vessel "Situation" from "Orbiting" to "Landed" at around the time of undocking.
This seems related to the bug that was reportedly fixed in patch 1:
Except in this case it doesn't seem like reloading the game is the cause, but rather undocking (i.e. splitting the vessel into two), at least in my case.
(Well... probably. I actually don't have any hard evidence that the undocking was when the problem occured, but it seems like the most reasonable option, since before it the trajectories were showing correctly and when I looked at the map after undocking, the orbit was gone. The saves mentioned above are from just before and several minutes after the undocking.)
Also, I found this report describing a very similar bug:
Maybe someone should merge them?