FST is the new real timeline by Honroy

When Jacob was killed and Jughead destroyed the island, it created the FST (flash-sideways timeline) as the new main timeline. The OT (original timeline) is still being experienced by the Losties on the island in 2007. However, the FST past experiences are bleeding into the OT, and the OT experiences are bleeding into the FST.

The producers have stated that Season 6 is much like Season 1. In Season 1, the characters experienced problems on the island, and as they resolved those problems, we were shown flashbacks for those characters that showed past actions that were affecting (or paralleling) their current actions. In Season 6, we are seeing more of the same. Look at Ben - in the FST, he helps Alex at the expense of himself and his power, and it is reflected in his actions on the island. His FST memories/self is what is driving him now.

Desmond's previous time-traveling was within the OT, but now when he goes to the past he goes to the FST, because it is the new real past for him (and everyone else). I think his two memories have merged, and now he is going to help the Losties in the FST (find them via the manifest and try to show them the OT) and in the OT (go with Sayid and help him remember the OST).

This might also explain why the MIB (or any of the Losties) can leave the island - if they leave, the enter the FST. Remember Dr. Chang and the rabbits? If the Losties in the OT meet the Losties in the FST, it could mean a paradox that destroys the world.