At the start of the series, we learned that when Thawne killed Nora, for some reason his powers faded. To get himself back to his own time, he took over Wells' life and caused the reactor accident five years early. This made Barry the Flash five years early, and increased Thawne's chances of getting back to his own time.
This time around, it's still the Thawne that killed Nora. Not a later or earlier version of him. (Barry just took him unconscious out of the house before he could kill her, and locked him up; it was this Thawne that Barry then released.)
Thawne kills Nora, somehow the earlier Barry doesn't stop him, Thawne brings present Barry back to the present, and then takes off.
Why are Thawne's powers still working? Shouldn't they have faded just like they did last time? Since they haven't faded, WHY haven't they faded?
And what about Wells? Did Thawne go back to that night and kill Wells or not? If his powers are fine (and it seems they are), then Thawne had no reason to kill Wells that night. So is Wells alive, or not?
If Wells is NOT alive... WHY isn't he? And if Thawne never took over his life, who played Wells over the time covered by the first season in this new version of the timeline?
Have the writers ROYALLY messed up?
By reversing her life and having RF actually kill her off, would that not just have everything fold back to what already happened before Flashpoint then?
Or would it not just creat alternative time lines that Flash would return back to his own, and have that other one continue on as is?
And is RF now a walking anomoly, as he manages to survive his own timeline death, and now is recreating a new future history for himself?