I think only Barry's world gets flashpointed...
Everything else(meaning arrow, Legends of tomorrow, SuperGirl, and the Central City Barry just left) stays the same. There will be a search for The Flash in one timeline, and Barry doing whatever in the timeline he went to.
I just think if they changed everything that it would be too confusing... I like confusing things, but even I think that it would be too much.
Or...
Everything starts to change in The Arrow finale tonight? The world heading to nuclear Armageddon sounds a lot like The Flashpoint movie.