In the main timeline, the Original Eobard Thawne travels to the past to kill Nora Allen, making him lose his speed so that he turns future Barry Allen into The Flash which is where the main timeline ensues during seasons 1 and 2. (The color of Eobard Thawne/The Reverse-Flash, yellow, mixing with the main timeline's sequence of events, blue, resulting in HIM losing his speed whilst having to eventually recreate The Flash himself, green.)
After Barry freed Eobard Thawne from Flashpoint, he traveled to the past as he killed Nora Allen, but he never lost HIS powers since he restored the original timeline as HIS was lost after Flashpoint was created, turning him into a Time Remnant who would later run into Legends of Tomorrow as he tries to steal the Spear of Destiny for himself so that he could rewrite himself into a reality where The Black Flash from The Speed Force would stop hunting him. (Eobard Thawne/The Reverse-Flash being left alone, yellow, because HE never got stuck in the past to warrant the green directional arrow from ever, actually HAPPENING to him.)
MEANWHILE, Barry returns to his typical future of becoming The Flash in HIS story that's copied from the main timeline, blue, thanks to The Reverse-Flash obeying the fixed point by killing Nora Allen, red, but it breaks Barry off of course AS he's ensuing into his new timeline that's taking place in a future after Flashpoint had happened, purple.