Eddie Thawne is one example of this. It's documented in history, as far back as Episode One, that Eddie loved Iris, but Iris never married him. How, then, did Eddie become Eobard's ancestor?
Conspiracy theory: Eobard is Nora's descendant!
The timeline shifted when Eddie died: Instead of Iris marrying Thawne, she married Barry. This means that if my theory is right, Thawne could have been changed in his future. This new Eobard could be named Eobard Allen, for all we know, and this means that the reason Eobard can never defeat Barry is because the timeline's trying to protect the both of them. The next timeline shift could be what turns Eobard into Godspeed!
Nora needs to come clean to her parents, as the bios state she will. Maybe, once the story is told, we'll finally be able to unravel the Gordian Knot of Eobard's existence, or maybe have Barry cut it apart permanently, though that would disappoint me. I like it when villains are redeemed . . . Except for characters like Merlyn. Why take away the best villain? My argument against Eo being Barry's arch nemesis is simple: Eobard may come back eternally, but he'll never be as destructive to Barry as Barry himself: Savitar, Flashpoint, Nora, and Seeing Red are just a few examples.