My assumptions on what CW is doing with The Flash are followed, they are just my opinions.
I'm going with the obvious assumption. In the comics and the movie Flashpoint Paradox. Flash goes back in time to save his mom. Sound familiar? Well doing so makes him lose his powers and makes a feud between the Amazons and the Atlanteans. Bruce Wayne died instead of his parents and Thomas took up the mantle of Batman while Martha took up the mantle of The Joker. While this is one of the the things that might happen, I doubt it to happen. I see CW making their own Flashpoint Paradox. Maybe Barry might lose his powers, maybe his father will die and his mother will survive. Maybe Caitlin Snow will get her Killer Frost persona, maybe the reactor would never erupt and Caitlin and Ronnie could have their marriage. Maybe everyone would forget the Flash existed thus killing him. This is what is fun about time travel, we just never know. Who knows what could happen? Could Barry really effect the timeline and mess up the world he loves, could he lose his speed? Where did the first Flash go to after failing to save his mom? Did Eobard kill him? Why is the Flash missing? These are good question. We know that Eobard needs Barry to be fast enough to equal him out, to reverse him. My assumption is at this point in the show they both are the same exact speed, but we'll just wait until Tuesday to see.