Look here for the video reference. In the Flashpoint, at the beginning of season 3 of The Flash, Barry Allen lets Eobard Thawne to go back to the fateful night and kill Barry's mom. Ok, here is the crucial part of changing a timeline.
The original timeline was changed by Barry at the end of season 2 by stopping Eobard from killing his mom (1:50). As a result of this event (of saving his mom) we see the Barry behind the door smiling (that his mom is now saved) and vanishing (2:11) because well, the timeline changed!
So, now we know that the timeline changes due to an altering event. (Pretty obvious, right?)
But when Eobard comes to kill Barry's mom again, we see that Barry and the other Eobard lying on the floor are both vanishing (2:37).
Wait, hold on! The new Eobard hasn't yet killed Barry's mom. So no event has yet occurred that could change the new timeline where Barry's parents are alive. Then how could Barry and Eobard (the one lying on the floor) vanish? This makes it easy for the new Eobard to kill Barry's mom without a fight from Barry. This is so not possible! No event occurred, so no erasing of timeline, and therefore no Barry should be vanishing yet!
What should have happened here is that the recent most Eobard and Barry, who agree that timeline needs to be reset come back to the fateful night and convince the previous Barry, who just saved his mom, to allow his mom to get killed or else fight him if he doesn't agree. Only after his mom is killed, should the previous Barry and Eobard (lying on the floor) vanish as only now the timeline is reset.
What am I missing here? Or is it that the show writers missed this plot?