As far as I know, the trajectorys vanish sometimes after undocking specific parts. I experienced this after undocking my launch engine (w fuel tank) tho i do not recall which one it was. Restarting didnt fix it for me, I had to go to the save file manually and change the state of my vessel from 'ground' to 'flying'. Maybe there is a problem in the detection system of the flight state after decoupling stages?