The thing is, the New 52 reboot was rushed compared to COIE.
COIE was a 12-issue event created specifically to clean house and combine what they wanted to keep into a new reality.
Flashpoint was a stand-alone “fix the broken timeline” story that grew. Somewhere along the line, DC decided to use it as the springboard to launch the New 52. They added a double-page spread with some mumbo-jumbo about merging timelines, and drew the new costumes on Batman and Barry for the last two pages. (I can’t confirm this, but given the timeline of when Johns and Kubert started Flashpoint, when the reboot got greenlit, the story of Flashpoint itself, and all the stuff Johns talked about putting into his Flash run that didn’t make it, this makes the most sense.)
In my mind, Flashpoint and the New 52 are completely separate entities.
And speaking of things that are completely separate…
“Francis Manapul and Brian Buccellato are doing amazing work.”
Yes. Yes they are.