Alternative timelines seems to be what they are going for here. It would explain why the earlier/different versions vanished when they arrived. They were shunted into another reality.

It doesn't explain however why RF would have even changed history in the first place because that just means that the original timeline is still playing out.
If that newspaper is right and that involved the COIE then Barry is dead and perhaps RF didn't do this just to mess with Flash's life but actually did it to get to interact with his old enemy again. In a perverse sense he might have missed him but didn't expect to lose his powers.

I think we will find that Dr. Alchemy is the reason RF is still kicking.