I don't think Jughead exploded until Desmond turned the fail-safe key in 2004. The EM/H-bomb interaction I've heard described all over the web (an implosion that would dissipate the EM pocket) sounds very much like what happened when the hatch was destroyed. The fail-safe device (IMO) *was* Jughead.
I think (and I know I'm not the first) that it's likely we'll return to 1977 and find out some of our Losties have been flash jumped out of that time period. Not by the Frozen Donkey Wheel like before, but by the same power that flash jumped them off flight 316 and into 1977 to begin with. On the plane, that time jump was accompanied by a white flash. During the Incident the white flash we mistook for the detonation of a hydrogen bomb was actually just some of the Losties being jumped to another time.
Not long after that happened, Chang probably ordered the creation of the fail-safe device using the bomb they found next to dead Juliet. Then a ton of concrete, and a weird computer system, 108 minutes for some reason, yada yada, and the Swan was born.