Pandora mentions in the splash pages (from the final issue of Flashpoint) that combine the three timelines to form the New 52 that Flash has to help her "fix" the timeline, implying that something is wrong. We don't know what that was supposed to refer to yet I don't believe.
I remember that - something about rejoining what should not have been sundered? That seems at odds with what the Stranger says here. Then again, it's not necessarily either/or: the timelines were supposed to be rejoined, but something about the way Zoom initiated it caused it to go wrong.
Then again I'm anal enough to be bothered by the suggestion that the Vertigo universe was unified: until I see Skinner Sweet fight Andrew Bennett, I'm not satisfied.