Re: DC's New 52: Reviews and Discussion (Spoilers welcolme and likely)
I don't see how Morrison would change any of the Legion's back story with Clark since we know that the current Legion timeline is intact from before. Remember two that Imra, Garth, and Rokk were referenced in issue one and were called by Clark's landlady "his friends". So I suspect that nothing will be drastically changed. It's possible that the amount of contact will have been decreased.
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Ignoring the The Last Stand since 2011.