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Have you tried increasing the maximum length of the trajectory lines? Depending on your model you might need it to trace the trajectories for a longer length. Depending on recirculation and the size of your model you can easily exceed the default.
Another (less likely) possibility is that it losses track of those trajectories. I've seen this when a trajectory line at high speed touches a solid body. Think of it as a particle study, that particle is now imbedded in the wall and can no longer move, hence that trajectory simply ends there.
they shouldn't end at a wall unless it reaches zero velocity in a particle study or its absorbed into a wall. I don't think that applies to the flow trajectory
increasing the length should solve the op's issue