Considering how top secret the Discovery is... I can see that Lorca won't realistically let crew transfer off Discovery, until the experiment, or the war is over, so there will be vanishing crewmen.
1. Crewmen that get sent off the ship, for reasons, are not returned to general matriculation, hell they could even be sent to detention facilities, while they wait out the war or this experiment, or they transferred parallelelly to another edge of the spore experiment.
2. The three prisoners, who were not Michael Burnham. Either they were fake prisoners to shape Burnhams narrative for Lorca, or they are being sent to the worst jobs on that mining colony to die quickly, or they are not going to a mining colony at all, but a dentition facility where they can't say anything about the Discovery or the "final" fate of Michael Burnham, until the experiment or the war is over.