Spoilers through "Happily Ever After"
So, after the last episode it's become very clear that the 2 realities are indeed connected as many have speculated. Characters in the Alt. reality are starting to remember on island events/people so the obvious thing we can draw from this is that whether the alt. reality was caused by the nuke or some other event yet to happen, the Alt. reality was born out of the island reality.
The question really is which reality will exist when the smoke clears (pun intended
) at the end of the show?
My personal opinion now is that the people on island will work to keep Smokey from being able to leave up to and including sinking the island somehow which will protect the Alt. reality which will be the "final" reality when it's all said and done. The only twist is that the Alt. Reality people will get back their full memories.