Hello Damian,
If the individual flight have considerable overlap with each other, the GSD is more or less similar for all flights and the conditions are also similar, then you can run alignment for all photos in the single chunk at once. Usually it's better, as the shouldn't be reconstruction artifacts in the flight overlapping areas that could appear in case of individual per chunk processing. Also if you are using control points you would be able to use the complete set of GCPs for the whole area.
Splitting the calibration groups may be reasonable in case of low quality optics, zoom lens and after hard landing.