I researched the area for the deposits. And went to sleep being happy. On a next day, after the update, this is what I see. The area, which I have researched, is now marked as unknown.
I gave it a chance. I thought: "it's a new version, it can be incompatible a bit." However, it happens on the game load after the game update as well. It's definitely not a save game compatibility issue.
Do I need to restart map scanning on every load?!