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When I start a new save and new character a bunch of the missions are already done for me. Is there a way to clear this or what would I do if I were to do a gen2 run?

On SE its impossible to tame an Achatina so that should be removed from the QoB list. Also Ovis are really rare on SE. It's easier to find a phoenix. I think Ovis should also be removed since phoenix is removed.