In Batman v Superman, Flash came back from the future to prevent the Knightmare timeline. This split the timeline, and I just want to explore that in writing.
There are three confirmed timelines. The first one is the Knightmare timeline. Everything up to the moment Flash appears before Bruce is the same in all three timelines (unless Bruce's dreams are a ripple effect phenomenon from the time travel as theorized), but the events after that are largely unknown. They do lead to the Knightmare as depicted in Batman v Superman: Dawn of Justice. In this timeline Flash doesn't come back from the future, as there hasn't been a future yet.
The second timeline is consistent with the entire DCEU so far, setting aside the theatrical release of Justice League for simplicity. Flash came back to warn Bruce, and doing so changed how events played out to an unknown degree, however, Flash came back too early in the timeline, and so the Knightmare wasn't prevented. This timeline also ends up in the Knightmare future. Any Knightmare scenes in Zack Snyder's Justice League will take place in this timeline, as Flash has already prevented the first Knightmare. There likely won't be any differences between the Knightmares, though. It would just get unnecessarily confusing.
A third timeline is then created by Flash going back a second time, this time meeting Bruce at the correct moment to prevent the Knightmare. This hasn't happened yet, but is a confirmed intention that may or may not make it to screen. The Knightmare never occurs in this timeline. This timeline, like the second one, is also entirely consistent with the DCEU so far (again setting Justice League aside for simplicity).
Zack Snyder's Justice League could reveal which timeline we're currently viewing. If the events of the movie lead into the Knightmare, it will mean we're in the second timeline, but if Flash appears to Bruce again, the entire DCEU will have been in the third timeline apart from the Knightmare clips.
As for The Flash, Flash again travels back in time to change the present. Perhaps he's emboldened by the success of his second-timeline self. He'll probably be creating new timelines, regardless of whether the Flashpoint universe is one of them. We may find out that the DCEU's third-timeline Barry Allen is the creator of the entire DC multiverse. If they thought it through properly, he isn't just going into the past and popping up in a separate universe, but rather, he's changing the past and creating a new timeline. That's all the multiverse is: a collection of timelines created by time travelers. The events of The Flash may create Batman (Earth-89)'s universe, Flash (Earth-1)'s universe, and any other DC universes they might include in the movie while Flash messes with time.