Flash season 3 episode 1 plothole?

Barry askes Thawne to kill his mom. That happens in the first episode:

Thawne 1 (not in prison) vanished and Thawne 2 (that one barry held hostage) is there and kills Nora but then as we know from Legends his fate is very different then fromt his fate in season 1. In season 1 he lost his speed but now he has it and he is being hunted by black flash which brings in the plothole: Where is Thawne? The Thawne in season 1 but also season 5 when Barry goes back in time with Nora because they need his help.

Where is he? So, is this a plothole? And for some saying it is a loop it really isn't.

It is one timeline and in that timeline Thawne says by by and he does not turn into Wells