After Watching the season 2 finale of The Flash, it looks like CW will be going with the Flashpoint Paradox storyline for season 3, but with some major tweaking because they can't reference Batman/Bruce Wayne/Thomas Wayne. So think of this more along the lines of Fringe season 4 and 5 rolled into one.
Okay things are going to get confusing so let me break it down in the simplest way possible, Earths, Timelines and Characters. Ready?
1. Earth-1 Timeline
The first and second season are no longer canon because Barry went back in time to save his mother.
2. Earth-1 Characters
- Harrison Wells (ALIVE)- Since Reverse Flash was stopped from killing Barry's mom, he will never kill E-1 Wells meaning that the real Wells is now alive in the future.
- Eddie Thawne (ALIVE)- With Eobard never becoming Wells his plan to get back home never happens meaning Eddie never takes his own life.
- Ronnie Raymond (ALIVE)- Again, Eobard never became Wells and the breach over Central City never happens, so he doesn't die saving the city.
- Nora Allen (ALIVE)- Obviously this doesn't need explaining.
- Henry Allen (ALIVE)- Since the breaches to other Earths never opened, Zoom never came over to kill him.
- Gorilla Grodd (ALIVE on EARTH-1)- No portals means Grodd never left Earth-1.
- Eobard Thawne (ALIVE)- Flash stopped him, but didn't kill him and since he never became Well, his death never happened at STAR Labs.
Okay this is going to seem weird but it makes sense. Even though Earth-2 characters interacted with Earth-1 characters, they are not affected by the timeline change. They remember the original timeline, not the new one. However, no one on Earth-1 knows about Earth-2 nor do they remember defeating Zoom.
1. Earth-2 Timeline
Here first and second season are still canon and the portals to other Earths still exist. They are aware of everything that happened in season 2.
2. Earth-2 Characters
- Zoom (Dead)- Since he is part of another universe and another timeline his death still happened, even though it happened on Earth-1 it was still part of Earth-2's timeline.
- Harrison Wells-2 (Alive)- He remembers Barry, going to Earth-1 and defeating Zoom.
- ***All other characters that were alive are still alive and those that died are still dead.
It should be noted that once Barry returns to the future he may not have his powers, if you remember, Eobard Thawne said he needed to move that date up by 10 years. So the explosion at STAR Labs could still be years off. But then again they used the Flashpoint Paradox method already to give Barry back his powers in season 2. This again falls inline with the fact that the FP storyline will be heavily altered.
If you are confused by any of this or think I left something out just leave a comment and I'll get to it as soon as possible. Because we have a few months till season 3 airs and there is nothing like fanboy speculation to pass the time.