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I wouldn't have both running together if I were you, it really wouldn't make sense story wise to do so because the Enclave in AR2 is really its own standalone faction. I think they should work together but it will definitely be bizarre when you have side along the Enclave and then decide you want to wipe out civilization. Really game breaking I would avoid and just have a separate save.
Yeah after reading up a bit on the quest line it would make for a very strange chapter 3 in Sim Settlements unless you choose to fight the enclave later on in their quest story. Thank for replying.