Turning the frozen donkey wheel exposes a person to EM and in essence resets time, like what Des experienced when he went back to 1996. One version of the body goes to one reality and the other in another reality. Version 1 of the person creates another timeline for the other version of the same person to exist in by changing time, making different choices and influencing the timeline. The fork happens in the past but it looks like the person splits instantaneously between realities and that's what happened when Locke turned the wheel and when Ben turned the wheel. Each man sort of splits to be able to appear in two realities, one which was what happened up until the wheel was turned and another which consists of the changes made by the person turning it. The purpose of turning the wheel is to correct the first timeline.
Let’s start with the original timeline, no one had made any changes and then Dharma sent someone back in time to make changes, maybe that was accidental after the first incident. Then let’s say that Widmore had a turn. Widmore decided to push people into making different choices because he knew what the future holds, he has already lived through the original timeline and gets déjà vu to guide him all because he turned the wheel and was exposed to EM. Then Ben took a turn and he had to change the things that Widmore had attempted to change. I think that it all has to do with setting up the scene for the final of the show. How the chess pieces fall in the end and who will be manipulated by the MIB and/or Jacob.
I think that after Widmore it was Ben’s turn. He turned the wheel before Locke should have because he thought that he could make a difference, outwit Locke’s plans and become the hero. I don’t think that Ben’s plans were just off island, like what we saw in him killing Locke and bringing them all back. I think he did much more on-island that we were not aware of. I think that in the timeline before Ben’s turn, Ben did not pretend to be Henry Gale. I think that this was one of the changes that Ben did when he reset time when he turned the wheel. He wanted to stop John from ever finding the cabin and getting the message to turn the wheel. Ben failed, the wheel went off it’s exis and John still managed to get his turn.
Ben was always saying things were not supposed to happen and so was Locke and they both turned the wheel. They were both at some point in the show, manipulating the timeline without anyone else's knowledge.
I say at some point because I believe that we have been watching a cleverly edited combination of timelines made to look like one continuous story. A combination of several timelines, each one with a different person controlling the events. I think it was the reason that certain people became leaders of the island because they had the déjà vu flashes and could see the future and make appropriate changes. They wouldn’t of course know the full consequences of their actions and all the possible outcomes of their actions, just knowledge of what happened last time. It’s why Ben didn’t think that Alex would die because the Others probably have a rule which covers changing other than what is essential to the end game plan – what we are about to see in the finale.
So now Locke has turned the wheel after Ben and he is now working on changing the timeline which Ben was in charge of. What Locke could not have foreseen was that Desmond was also exposed to EM was also messing with the timeline. At this point I am not theorising whether Locke is working on behalf of MIB, is even under his influence or has evil intentions. All I am suggesting is that Locke knows some of future events, some of what should happen in the future. When Jack is at the radio tower waiting to get a signal to contact the freighter Locke is saying to Jack, “Jack. You're not supposed to do this.” I believe that John could see that if they left the island then there would be a future which was not desirable in his opinion based on what he could see of the future.
Desmond of course was also getting déjà vu moments. I am assuming at this point that Desmond was interfering with Locke’s plans but it could be that I am wrong about there being only one person in each iteration with the future flashes. Perhaps in each new iteration of the timeline the people who have previously turned the wheel can still see the future. It would explain why Widmore is still able to be in the game since he’s come back on the sub. It might also explain why he is so wealthy off island if he can see parts of the future – great business tool that one. Therefore it could be that Des, Ben and Locke were all working with future knowledge and perhaps they were all getting flashes to the future.
The reason I think that one timeline replaces the other is from what we’ve seen of sideways.
I believe that sideways (the timeline we are watching off island) is the Losties turn at making different decisions. They were exposed to EM at the incident (which is the same as turning the wheel IMO) and they are making different decisions because of the déjà vu they are experiencing on a sub-conscious level. EG Frank remembered to set his alarm and did not sleep in, he made it to Flight 815 and he saved the Losties from crashing on the island. Sideways is a collective sub-conscious effort from all the characters exposed to EM to make a change to the timeline.
The only thing I do not like about the theory I present here is that it would follow that the sideways Losties need to get back to the island again. Perhaps they need one more exposure to EM, one more reset and attempt to do it again. Perhaps the version of the timeline where the Losties have a view of the future was also woven into the story we have already seen or perhaps it will be shown to us by means of a montage of scenes from pivotal moments, or crossroads in the show where our Losties (with the benefit of EM induced future knowledge) can chose a different path to change the end game of Lost. Perhaps the Losties we are watching in the final scenes are these enlightened versions of themselves already. In the idea I am presenting for the whole show to make sense, one would need to watch the show again and probably re-watch it as many times as their have been resets or rather I should say as many times as people have been exposed to EM and have reset time.