Re: Smallville Season 11, it"s happening...
I understood the point that you're making Proc. I just don't really think it's that big of a deal. The Legion also utilize time precision technology. As I mentioned they would just return Micheal and Clark to the point in time where they were originally departed from. AJK mentioned "Back to the Future" as a prime example of this. No one will even know that they were missing. The only way that you're scenario MIGHT occur is if something went wrong with Brainy's calculations "Doctor Who" Tardis style...then maybe Clark missing might be a factor. Otherwise...he hasn't missed enough time to have any kind of major effect on the timeline as a whole. If that were even the case...the Legion and Brainy would not risk plucking Clark from his native time period. As you say restored Clark's naturally flowing history, as I've already mentioned still is intact.
Chief of Operations
Ignoring the The Last Stand since 2011.