The whole Flash-Sideways thing has given me a headache, and it was annoying me. But, for some reason, watching the final Missing Pieces episode has helped me make my peace with it. It's the one that's set just before the original crash, and Christian tells Vincent to wake Jack up: "He has work to do..." I think that this has - not changed my views on the FS etc - but it's allowed me to make peace with it. As if everything that they have done has been with the purpose of creating themselves a second life. This isn't a theory, but more so me sharing what has helped me deal with the annoyance of the FS revelation.