Perhaps I'm just not understanding the documentation, but I copied a building, pasted it, found it did not copy all the entities, so I typed /undo as I wanted to remove what I just pasted. Instead it removed the entire building that I copied from, not what I had just pasted.

are you sure you were looking at the right building? this shouldn't generally happen. was there an error in your rcon/console when doing copy/paste?

I was across the map when it happened. No error that I saw. I was at an ice lake, I had something I'd built there so copied it and I teleported to a different ice lake to paste the building to make sure I got everything copied. I ended up not setting the radius large enough in my initial copy so I just typed /undo. Instead of removing what I had just pasted, it removed everything it had copied back from the original base.