Right, this has happened to me again just a day later. After clearing the new battle tower, I went out to explore before returning to my base hours afterward. I return to find a new battle tower next to the former battle tower and see that my base has once again been replaced with solid stone blocks.
One thing I did that I forgot to mention last time was to explore a dimensional dungeon. I died, got a "your home bed has been obstructed" message, then fell into Limbo. I don't know if it's related or not.