I took some time on my new save to further the Artemis path while collecting more Salvage to purchase blueprint items.
When the story took me to the Anomaly for the second time, I finished my business there and decided to portal back to my Home base I and resume building. The Nexus portal took me to my station, and I took the station portal to my base. It was clearly mark on the port and I landed right where my base portal should have been.
However, when I arrived through the portal, not only was my base gone, but the base computer, the small refiner, the organic engine thingy, and the portable construction thingy, were gone. The whole thing as if they had never been.
EDIT: I forgot to mention that I built a second base in a different system a couple of days ago. Therefore my question in the title.
Has anyone else had this happen?