Here's a thought about the two timelines, and how they could end up merging into one.

Remember when the oceanic 6 needed to go back to the island, and Eloise Hawking told them they needed to make the flight as similar to the original as possible? Perhaps the act of creating similar circumstances was in fact a way of "course correction." The flash of light the Aijra 316-ers experienced was not only them traveling to a different time, but a different timeline.

Think about it. If the ALT was created in 1977, when Aijra flew over the island in 2007 the two parallel universes already existed. For Aijra 316 to end up in the correct timeline/universe (the timeline where 815 crashed onto the island) they had to make the circumstances correct for that timeline. Also, remember the season 4 finale? Everyone describes the island as "disappearing" but it doesn't really disappear. It sinks. Let me say that again...It sinks, as in underwater. As in, where it is in the ALT timeline. (Ok, I'm not sure how that ties into it, but I thought it was a cool observation.)

The idea of parallel universes and course correction could offer a way for the ALT losties and the original losties to merge. I do believe they will merge, as "doubles" and "twins" have been a big theme from the beginning of the show. Also, remember Dr. Marvin Candle's film with the two bunnies with the number 15 on them? He said not to let them near each other. Foreshadowing? I think so. Anyway, the ALT Losties could possibly course correct so that they could reach the island in the timeline/universe where it is not underwater.

This is a pretty convoluted theory and I'm having trouble organizing my own thoughts around it. More to come later if I can sort it all out.