The last game update wiped out the efforts of the factions to finish the game. The Anu Temple was under construction. It disappeared. The Schneidreian(?) moon mission was under construction. It disappeared. They were not attacked. They just disappeared from the map. Have had to restart the game.
Had something similar happen with the Year One update. Was ready to fight the last battle. The update prevented loading the saves making me restart the game.
Also, I wish the developers stop making it more difficult to fight the Pandorians. The latest update stopped piling on Mark for Death making Skylla more difficult to kill than they were before. Saw the same thing with the Rage Kill change which has made Rage Kill useless.
That was only with one major update, you should report your case ingame as bug.
It was other way around - massing MOD was a bug, that is fixed. It now works as intended (1 MOD per target in one turn). Scylla is supposed to be hard to beat, use granades and launchers to lower armour, then next turn MOD and shoot at 1 limb until destroyed, and keep shooting that spot.