Several players complained (rightly) that NPCs on the Mothership Altair were going missing. As it turned out, this would happen after completing the quest in the first slot for each one.
I was able to identify the code that was causing this aberrant behavior, and remove it. Now your NPCs should stay put.
Also, random NPC quests on the mothership should no longer trigger the main mission quest requirements. However, if you complete a quest at the main mothership interface (from your ship) or complete a quest for Dr. Ignatz, or Commander Makki, (on the mothership) those will trigger the main mission requirements.
There is another, unrelated issue which will cause all the NPCs in the mothership to disappear. This can happen if the game is interrupted when exiting the motheship. I am still working on a system that will recognize a corrupted file and take measures to make sure it is not used. Until then, there is a pinned post about fixing some of the game's outstanding issues here: https://steamcommunity.com/app/502720/discussions/0/5800060047335778793/