that future ceased to exist
No it didn't. So far that is the New Future, after Future Peter went back in time to shoot Nathan. He was from a future where mutants were hunted and experimented on. In the New Future, the syrum was made, and everyone has powers.
The show will of course be about stopping the New Future and Old Future from happening, but so far, the New Future is where everyone has powers and Sylar
hashad a son.
Don't forget...
Before Matt had his
dream about New Future (last episode), the Painter repainted the future, as it had changed.