I think fighting the cloned generals is the problem, I believe your savegame has become corrupt due to it. Try to teleport them away to a safe location instead, there are some remote areas in the Sahara and Indian sea you can exile them to where they can't get into fights. Bring them back once the clone is dead. You may want to disband a number of your own units to simulate your fighting the army.
Remember to keep earlier savegames with intervals of 4-12 turns, so you can step back and hopefully avoid that the same crash conditions occur again.
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