So, what does this warning mean? I just tried a new map, Fruechtparadies (I assume that means Fruit Paradise). It loads with several additional mods for equipment. When I opened it and played a bit everything looked fine, but when I tried to close the map, FS closed, without going back to the main menu, and the warning above came up. I deleted all the mods including the map and went back to the game. Everything worked OK. I reloaded just the map without the other mods, and the same thing happened with the same warning message. I did think to try loading another map, and it worked fine and the game closed fine.
So, I worry about what this is doing. Changes I made in the Fruit map were retained, so it at least appears to be working correctly, but the last thing I want to do is damage the game or other savegames.