On the first Tulou mission, leaving the system will cause the woman at the station to act like Tian is dead, even if he's alive and in the system and you completed the mission. Tian will continue to follow you (until you leave him behind or he dies).
Commonwealth Militia missions to destroy a station will act like you failed, even if you completed the mission.
Leaving the system during the battle with Luminous causes your allies to retreat and makes the mission uncompletable, even if you destroy Luminous by yourself.
Thread with a slightly different version of the final Luminous mission problem:
https://forums.kronosaur.com/viewtopic.php?f=18&t=8668.
Fixing this might require missions to be able to fire an event on failure or if the player is out of a system for too long. But maybe we can just remember the tick the player leaves the system and adjust things when they return based on how long they were gone.
I don't remember exactly how the mission goes, but if the fighting hasn't started yet, maybe the allies should just wait indefinitely for the player to return. If the fighting has started, then either they need to retreat if the player retreats (complicated to simulate) or we just presume they lost if the player has been gone too long and delete them, but allow the mission to continue.