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One of the common issues that can be solved through post-processing is the linking of the broken trajectories. There are publications by Beat Luethi (called glueing) and Haitao Xu (multi-dimensional tracking) that dealt with this problem for 3D-PTV specifically and there is an old Matlab code that I've wrote some time ago
The idea is rather simple - for each two trajectories that are possibly broken pieces of the same trajectory project the edges (last for the earlier and first for the later) towards each other and see if they are within the acceptable tolerance (of distance, velocity and/or acceleration and time difference). If they are, connect, replace them by a single peace, make it smooth again, repeat the search.