I think that the whole thing about Jack recognizing Desmond, and Kate recognizing Jack isn't them remembering them from the original time line. I think that the losties have previously met in their new altered lives. The losties are bound together by fate, and their paths crossed many times before they crashed on the island in the original timeline, and I think their paths crossed just the same in the ALT.
So I think that as the flash sideways' progress, we will start seeing flash sideways flashbacks. In these flashbacks, we will be shown how the losties' paths have crossed in the ALT. I think they'll also show things like whether Jacob and MIB is in fact alive in this universe, and whether the others ever got off the island before it sunk, assuming the bomb didn't make it sink. And of course, the most anticipated question of the ALT, why is the island on the bottom of the sea?
This is all assuming that there is in fact and ALT, and not one timeline.