The reason is, when you first start a patrol or mission, the game reads the resources it has available to it, and then generates the game world based on those resources. So from that point on, the game expects to draw on those specific resources as saved by your saved game.
When you change the games resources by patch or by mod, and you load a saved game, its calling on those resources which are no longer present, hence not knowing what else to do, the game crash's or does wierd things. This is why you do all this stuff "in port" before the game calls on said resources to initialize the game world.
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