The Butterfly Effect -- a MAJOR reset by Merell

The explosion of the hydrogen bomb does indeed reset time, but not in the way that Jack, Daniel or anyone else imagined.

They thought the only change would be a singular chain of events: The incident doesn't happen, therefore the Swan is never built, therefore Desmond never crashes the plane. As a result, the only consequence is that everyone lands safely at LAX.

But as the "Butterfly effect" theory shows, every broken butterfly wing cascades into untold changes in the time continuum.

When we next re-visit 2004 in Season 6, everything is different. There may still be an Oceanic flight 815. However, the doctor on board may be Sawyer. The flight attendant may be Kate. Perhaps Claire has already been stranded on the island for years (cf. latest ABC promo). Characters we previously saw as dead are still alive, but in completely different situations.

Everyone is in a different place. The new "flashback" mechanism shows each character's new history and how they came to be where they are.

This is the first half of the season. The second half consists of everyone's stories coming back together to resolve the war between Jacob and MIB.