The Generation section of the Patch Notes states that the galaxy was regenerated and also that bases were repositioned due to terrain changes.
The galaxy regeneration is similar or the same as with the changes in the Foundation Update. The distribution of minerals, flora and fauna were completely changed, presumably due to the new additions as well as changes in the probabilities of generation. Thus planets' flora, fauna, environment, etc., all changed which accounts from going from barren to bountiful or visa versa or anywhere in between.
Based upon comments elsewhere apparently the tasks from the initial base building have to be repeated in order to receive credit for these having been performed for Atlas Rising. Others have reported that blueprints, quests, etc., are basically archived until the specialist terminals are rebuilt, hence re-staffed, and initial tasks are completed (again). It is unclear if having to repeat the tasks was by design of not.
Serren: I had the same thing happen when trying to teleport to my base so I manually flew back to it only to discover my lush beautiful world is now an ugly, barren ball of rock and all of the personnel in my base is missing. I did notice that the game is harassing me about hiring an overseer and building a base in the mission log too, as if I don't already have one.