Jack's bomb worked, as shown by the Oceanic Airlines commercial from Comic-Con. Season 6 will take place in 2010 (as hinted at by the episode 601 title "LA X", X being the roman numeral for 10) in an alternate timeline where Oceanic 815 never crashed. The characters who died on the island originally will probably find alternate ways to die in the new timeline, and the main survivors will be haunted by the island until they somehow return again. This is supported by Eloise Hawking's insistence that the universe can "course-correct" itself.
Meanwhile, Ben, Sun, Lapidus and company will still be on the island in the original timeline with fake Locke and dead Jacob. Whatever their immediate actions might be, they will live there until the other 815 survivors return in 2010. At this point, these two parallel universes--the original Ben/Sun/Lapidus one and the new one created by the bomb explosion--will have course-corrected enough the fuse and become one.
The problem is that even if all the characters can organize themselves correctly again, there is still a major difference between the two universes which would need solving for fusion to become possible: In the original timeline the island is whole, but in the new one it must have an enormous crater from the atomic explosion. This will be evened out by a catastrophic eruption of the island's volcano which will take place in the original timeline and cause enough damage to parallel that of the atomic bomb. This has been hinted at by Olivia Goodspeed teaching DHARMA schoolchildren about the volcano in season 3's "The Man Behind the Curtain".
Difficulties with this theory include Sun--will she die in the new timeline so that there will not be two of her when the timelines fuse? It seems unlikely that she would fuse into herself or something...