The Flashpoint story takes place in a completely altered universe than the normal DCU. Basically, the multiverse refers to a shifting number of alternate universes that coexist within the larger reality depicted in DC comics. Originally, these multi universes were created to explain various contradictory changes and continuity errors the characters experienced over the decades. So now, those characters are allowed to have several different versions of the same characters to simultaneously exist and, occasionally, interact.
According to IGN, “In the Flashpoint timeline, the world has been brought to the brink of destruction by a prolonged war between Atlantis and Themyscira. As Wonder Woman and Aquaman’s armies fight on, only Barry Allen retains any memory of the world as it once existed. But with his speed powers gone, Barry is forced to join forces with heroes like Batman, Cyborg, and Shazam to fix the timeline and restore the true DCU.”
They continue, “Flashpoint hinges on the revelation that it was actually Barry himself who caused this new timeline. The amnesic Barry eventually remembers that he used his speed to travel back in time and save his mother from being murdered by Reverse-Flash. That act caused a major butterfly effect, forcing Barry to accept that time isn’t to be meddled with, no matter how noble the meddler’s intentions.”