I think in yesterday's "The Flash" episode, Dr. Wells who was shown at the end of the episode was the real Dr. Wells (the good one) who was alive in the future world because when Eoward Thawne killed Dr. Wells by doing time travel, he created a new parallel universe and thus the actual Dr. Wells is still alive in the other parallel universe.
I hope everyone understands what I am talking about because its really getting confusing in this new season of Flash.