One thing I don't think we are taking into consideration is this: remember the 2024 newspaper in Gideon's archive? That we were led to believe was from the original timeline, the one in which Barry's was never murdered by the Reverse Flash. After all, it says the Flash disappeared, in which we now know was him going back in time to save his younger self.
However, there was only one moment in the entire series in which that newspaper changed...It's when Blackout temporarily sapped Barry of his powers, and Barry initially decided not to try and regain them back. Thus when Eobard/Wells checked the newspaper, he not only saw the lead story was different, but that there was no records whatsoever of the Flash.
Which means the 2024 newspaper is from the current timeline. Which also means Future Flash is from the current timeline, not the original one. This explains how Future Flash knew Barry was there and warned him not to interfere. But if Eobard, who comes from the future, remembers a different history, including that the real Wells created the particle accelerator in 2020, then how can the 2024 newspaper also be from his future? Remember, Eobard, in order to get back to his own time, recreated the conditions for Barry to become the Flash at an earlier age. Once Barry became the Flash, then history began to correct itself to lead towards that same future as depicted in the 2024 newspaper. Basically, think J.J. Abrams Star Trek, in that although the events in that even though the history of the Enterprise crew was different, they still got together to go on their voyage in exploring the galaxy, just like in the original timeline.
This also means that, in spite of Eddie Thawne shooting himself and thus erasing Eobard Thawne from existence, the Reverse Flash will still return and kill Barry's mom. How? Well, what have we seen happen whenever Barry travels through time? He remains unaffected, with his memories still intact. Also, as long as he's traveling through the Speed Force and time, he's shielded from whatever affects and changes are being done to the timestream.
The same thing applies to the Reverse Flash. So if an earlier version of the Reverse Flash was traveling back through time via the Speed Force, then he should still remain intact even though, paradoxically, he has ceased to exist. To take a cue from the comics, when Flashpoint happened, I believe it was explained that the reason Reverse Flash still existed, still had his powers, and still retained memories of the original timeline in spite of the changes is because he was protected via traveling through the Speed Force while those changes occurred. Same thing could happen in this case.
Also, remember the Reverse Flash who Barry faced in this season is someone who already has a long-standing history with Barry. Just like River Song in Doctor Who, Barry may have already just met Eobard, but Eobard, technically, hasn't met Barry yet, but will. This is also how the show could bring Matt Letscher as Eobard Thawne for next season, the difference being he's playing Eobard from earlier in the timeline who, because he was traveling through the Speed Force at the time his future self was being erased from existence. Which means he's literally a man out of time who no longer has a future to go back to. This can be the explanation for why the Reverse Flash hates Barry because he blames him for literally taking away everything he ever knew, even though ironically, it was his own great great great great grandfather all but forgotten by history. This would also explain why his Speed Force went out of whack once he killed Barry's mom--because he's now inadvertently set himself on the path where he causes his own death as we saw at the end of this season.