In S2 Finale, one could have noticed that the Future Barry only fought Thawne and sped his younger self out of the house. There wasn't a scene where a White-Symbol Barry stops Red-Symbol Barry from interfering, the one we saw in S1 Finale.
Obviously, THAT Barry was back from the 2020-Flash timeline, and he doesn't really exist nowadays.
I think the final scene of the Flashpoint will be different from the one in the comics. Instead of Barry stopping himself running on the cosmic treadmill into the past, it will be Barry stopping himself from saving his mother in 2000, THEN stopping and recreating the scene he remembers, where the 2020-timeline Barry stopped the Red-Symbol Barry. This will complete the timeloop of Thawne's time remnants, but because of Flashpoint's specifics, Thawne will still be resurrected when the new timeline is made.