See, this is why many Flash fans hated the whole Flashpoint storyline in Season 3 because it pretty much messed everything up and not a lot made sense after. Watch this video and you will have raised both your eyebrows!
WARNING SPOILERS AHEAD: (I prefer you watch the video)
If you want the short version, Basically when Barry traveled back in time and saved his mother, he created Flashpoint and he kept Eobard Locked up in the present. When starts to lose his memories, he asks the Reverse Flash to kill his mom. When they go back to that night. The old versions of them fighting vanish meaning those versions of them no longer exist. The other version of Eobard kills his mother and they travel back in the future and things are different. Now, This makes sense but THIS is where the plotholes starts to form, what doesn't make sense, if anyone Watched DC Legends of Tommorrow Season 2, Everyone knows Eobard Thawne showed up to form the Legion Of Doom with Damien Darkh. It has been confirmed that is the SAME Eobard whom Barry trapped in the Flashpoint alternate timeline when he stopped Eobard from killing his mom. The issue is that version of Thawne logically would've never became Harrison Wells and he would've never been able to killed Earth 1 Harrison Wells by this logic because everything was affected and screwed up during Post-Flashpoint. And this creates an even bigger plot hole because if Eobard Thawne never pretended to be Earth 1 Wells when he went to appear in Legends this means, Eddie is not supposed to be dead thus making this plothole the biggest plothole in the Arrowverse. Now nothing makes sense. And it all started when the writers made several mistakes with the Flashpoint Storyline in the Season 3 premiere. Some might ask, if the Eobard on Legends is the same Eobard, couldn't he just have traveled back in time to restore the cycle? That's the only way the cycle could've happened but the problem is THAT Eobard was killed by Black Flash so he couldn't have done that. Now there's another Eobard who shows up in Crisis On Earth X which makes the plothole grow.