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The PvP neutral combat option can be enabled at the start and disabled when loading a game, and vice versa. It could be implemented so that the choice is tied to a specific game and saved in the save file.
Regarding incorrect unit placement, can you guarantee that both sides have 3.808f, and not 3.808f and 3.807f, for example?
In any case, compatibility with older versions needs to be cut for 3.809. I wanted to do this for 3.808, but I didn't, because firstly, it's not a fully-fledged release (no online updates), and secondly, players always have a hard time with such transitions.