I had this happen, too.
I used an older save, entered the Battery from the end and walked back to the entrance level. This worked. Same if I enter the middle level and walk back. It even works if I:
Enter top level - Map reset.
Go out again.
Enter middle level - Map still cleared.
Walk to top level - Map still cleared.
To my Unity-clueless self it looks like the option to enter from top level creates kind of a new instance of the same map.
Here's my save.
(Still 2.0 though, I don't dare to update, I like my Sagani.)
Here you go.