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When the losties blow the bomb maybe they do reset every thing.... but i don't think it deletes the timeline that Sun and Lepidus are in. I think it just branches off onto another timeline.
In 1977 Jack, Kate, Sawyer, Sayid, Jin, Faraday, etc. They all die there in 1977. BUT... they do stop 815 from crashing in 2004. John Lock is dead as well, but in a different timeline, (i feel like i sound like faraday right now) And now the universe needs to "cause correct" itself. So i think that that timeline, where Sun is "an other", Lock is dead and Lepidus is the new leader of "the others", - that timeline will eventually somehow collide with the new timeline where Oceanic 815 lands in LAX. Jack and them will eventually get back to the island. Perhaps they will all meet by way of the temple or something.
This would also fit with the light and dark. Remember that Jack described his experience (since he got to the island the first time) as misery. so maybe in the new timeline it will be joyful.