David Yudkin said:
Since they dragged Desmond out there and there are multiple timelines established, Faraday can't be far behind (with Desmond being his constant). He could probably get everybody back on the same page, but the question will be what each individual ends up as (if alive) after they spit out a unified timeline (or if they invent an altogether different timeline for each character).
I read one guy suggest that when Desmond turned the failsafe key on the Swan hatch in "flashes before your eyes", perhaps he flashed to an alternate universe. In that episode, he acted like everyone has been acting in the alt universe in season 6. In S6, Jack notices bumps and bruises on his body. In S6, Sun feels an odd bump on her head. Well in FBYE, Desmond vaguely recalled events of his island life, but was unsure.
Charlie dies in a scaffolding accident which REALLY didn't make sense at the time because we know he made it to the island, but it DOES make sense if Desmond flashed to an alternate universe. In the end Desmond gets hit with the cricket bat in the bar and then flashes back to the island, only he still has the bruise from being hit with the bat. Maybe flashing to an alternate universe also explains why he woke up in the jungle with no clothes on. Although I have no idea how.