Since the last episode of The Flash ended with Flash running into the portal, and the creators of the show have said "because of the singularity anything is possible on the show."
The way I think season 2 episode 1 will play out is we start out sort of like after the Flash saves his mom and changes the timeline in the movie flashpoint paradox. So Barry wakes up in his normal job or at his place and the tv is on the news and something with one of the rogues is on and he doesn't have his speed and can't do anything he remembers all this stuff from season 1 and nothing is the same in this world so while he's fumbling around trying to figure out what's going on somehow he runs into one of the S.T.A.R. Labs crew and asks "what happened why is everything different?" And they just say something like "do I know you?" And Barry looks absolutely shocked that they don't remember him. Eventually a parallel arrow (since batman hasn't come into the cw universe and probably won't) is confronted by Barry if they did this sort of thing it might be like Robert queen or Malcolm somebody that could take on the role of arrow besides Oliver and when Barry realizes it isn't Oliver he gets even more confused. That's as far as I've come up with so far tell me what you guys think.