That would be fine enough but the question posed was the role of the Particle accelerator, which I can only assume did not exist in the original timeline or Thawne would not have had to manufacture the 'accident' as a substitute for whatever event originally gave Barry his power.
If you accept that the original timeline had Barry gain his power by some random event (hit by lightning, doused in chemicals) and that his foes were the the traditional Rogues, and others like them not created in the new timeline by the Accelerator explosion, then the original Barry Allen/Flash would be something in line with the comicbooks - self confident, self-taught, and a very capable superhero whom the Reverse-Flash fought many times and was unable to overcome. One of the points about Thawne's interference in the timeline has been that his actions damaged Barry's self-confidence and ability to move forward with his life. This is something that has been noted independently by the Harrison Wells of Earth-2. So the influence of Thawne on his old foes revised timeline has been as profound as his impact on his old foe himself. In one sense Thawne did finally score a significant victory then, by killing Nora Allen and altering The Flash's life forever...
It's clear from Season One's 'Tricksters' episode that Wells and his wife do create the accelerator in the original timeline, just 20 years later. Thawne explains to the real Wells just before he kills him that it's his '...way home'. The implication is that he's using it to create the Flash in exactly the same way, just ten years early. The big problem for me is: Even if he could replicate the dark energy release, how does he ensure that Barry gets hit by lightning at EXACTLY the right moment? Especially given that Thawne has no speed at that point.
As for the original timeline no longer existing, I don't see why that should happen. Nor why the pre-Flashpoint timeline would get 'overwritten' by the Flashpoint timeline. They're nothing more than divergent realities. But Earth-2 is a divergent reality too. So is Supergirl's timeline. And Jay Garrick's Earth-3. None of those realities cease to exist just because another reality comes into being.
There is a difference between alternate timelines and parallel universes, at least as far as DC-Comics is concerned (and I ignore the effects and the diverse reboots of the Crisis):
The parallel universes existed from the beginning of the Big Bang as separate entities with their own complete space-time continuum, even if they had identical or mostly identical histories up to a point. There is no real divergent point where the timelines split ala Everetts Quantum Multiverse involved.
The universes of Earth 1, 2, 3 always existed on their own.