The only reason Thawne went back in time to kill Barry's mom was because of their rivalry reaching it's apex, which preceded him actually going back to actually kill Nora and change the timeline.
Nora was not supposed to be dead.
And Flash continuity was pretty consistently the same after COIE, outside Jay being around, which made sense since it was building on that continuity with Wally becoming The Flash.
Which he would not have done if Thawne hadn't killed her in the first place.