Here's something I know hasn't already been said here on Lostpedia.....
The white flash at the end of The Incident was a flash, caused by Jacob's death, that corrected everything that wasn't supposed to happen, i.e. the Oceanic 6, Desmond and Lapidus leaving. None of this was supposed to happen so season 6 picks up at the end of season 3 and shows what was meant to happen, whatever that is.
Jacob/the island had course corrected things as best they could before. The Oceanic 6(-1) were brought back to the island eventually. If Jacob hadn't died things would have course corrected themselves completely with his help, but because he died he used the last of his power to completely reset the island to where things started to go wrong, to when Charlie turned off the jamming equipment.
All the important people, including Charlie, kept their memories of the events that took place after the jamming equipment was turned off, so they know not to make the same mistakes again.