As someone who had a lot invested in the old DCU, I was pretty dead set against this at first. Flashpoint was a disappointingly perfunctory revamp that didn’t really wrap the previous DCU up in a satisfying way the way Crisis on Infinite Earths did, and so I mostly just kind of disengaged, except for a few titles that weren’t really related to what I was reading before like Frankenstein and Demon Knights.
That said, I found the collection of the first six issues of Geoff Johns and Jim Lee’s Justice League in my local library. I generally believe in not dismissing things unfairly because of NERD RAGE, however justified, and not blame particular stories for the bad decisions that set them up. After all, I thought Identity Crisis was an ill-concieved mess from start to finish, but it led to a lot of worthwhile stories like Villains United and 52. So I checked it out. These were my gut reactions more or less as they occurred to me.
Theory 1: The post-Flashpoint earth is actually a pocket universe/dream bubble Barry Allen ended up in, like the one the JSA was trapped in for a while as per Sandman: Season of Mists.
Theory 2: After his defeat in Final Crisis, Darkseid hooked himself into the Anti-Monitor’s corpse and Omega Effected the entire DC Earth, sending everyone to a different Earth. Barry Allen ended up in the Flashpoint earth, Batman wound up on the pre-Scratch Earth-Homestuck where he became Fedorafreak and then ascended to God Tier. This applies to ordinary people too—Grant Morrison was once a perfectly ordinary denizen of the DCU.