If I understood Thawne's video correctly, his big breakthrough was figuring out a way how to change the timeline without changing his memories of the timeline, but isn't that just the way time travel always worked? For instance Barry still remembers the pre-Flashpoint timeline, and Nora remembers her timeline even though she also changed it...
Maybe he figured out a way to retain his memories if someone ELSE changes the timeline. Barry never lost his memories of things he changed.