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1. I think the concept of Flash changing the past, with the intent of correcting the present, but not quite getting it right could work. What I'd really like to see is a "What If"-like chain of causal events that explains what Barry didn't get right, and how that impacts the new universe. Just running fast doesn't work for me. He inadvertently changed X, and then that changed Y , which lead to Superman being "reinvented" would work to bridge old and new. There is nothing wrong with an alternate universe diverging based on screwing up something in the past, this has been used in comics and movies many times. It just doesn't ring true here just yet.
Barry undid any change of the timeline by preventing himself from exiting the timestream to rescue his mom. Instead, some unknown-as-yet female (hopefully NOT Barry's mom) used the event to bring about the DCnU, for an some unknown-as-yet reason