What if we have it backwards? What if Seasons 1-5 of Lost are the results of such a controlled, messed up timeline (thanks to Jacob) that with all the altering going on, it's caused all the discrepencies we've seen throughout the show (such as object placement changing)? This timeline where Desmond caused the crash of 815 and the Losties to be on the Island really did save the world from ending in 2004 after Desmond activated the fail-safe, which then led to events where the Losties were sent back in time (Desmond prolonging Charlie's death enough for him to let the Freighter come to the Island), but if one hadn't happened, leading to the other, then the world wouldn't have needed saved. Ms. Hawking has been working so hard to preserve this timeline from the Losties and Jacob's mistakes just so the world won't end, since if even one event had changed, it would have caused a devastating paradox and "God help us! all". If this loop had never occurred where the Losties go back in time/Desmond activating the failsafe, the world wouldn't have been in danger--Dharma would have gone about their work, Flight 815 wouldn't have crashed, the Losties would have lived out their lives off the Island, and Desmond would have married Penny after buying the ring.
Maybe the Whispers are from the real, unaltered timeline and Season 6 will be about the battle between these two timelines. We'll see people who are dead in the manipulated timeline be alive in the unaltered version. Can timelines try to merge now that all the events in the altered and ruined timeline are done? Imagine all the differences in these two timelines of who is dead/alive and how even the smallest of events played out.
Maybe the Whispers are from the real, unaltered timeline and Season 6 will be about the battle between these two timelines. We'll see people who are dead in the manipulated timeline be alive in the unaltered version. Can timelines try to merge now that all the events in the altered and ruined timeline are done? Imagine all the differences in these two timelines of who is dead/alive and how even the smallest of events played out.