There has been one timeline 'problem' that has always bugged me. In 'The Constant', Desmond goes back to 1996, yet there isn't any confirmation that it happened in the real timeline. It's not like Daniel remembered meeting Desmond at Oxford (granted, his memory is a bit shot), and neither Penelope or her father ever mention talking to him.
Think about it: if regular 1996 Desmond spent a week running off to Oxford, wouldn't present day Desmond remember it? Not necessarily remember that week, but remember going back from Oxford to the army, remember people asking questions about why he was away, etc. (and by the way, when I say a week, I'm not exactly sure how long he actually was in his 2004-mindset). How can we be sure that the these events didn't actually happen in the original timeline?
Also, in Desmond's time in 'Flashes Before Your Eyes', we know that Desmond changed the timeline, or at least changed a different timeline: in the original timeline, Des recalles that Jimmy Lennon hits the bartender with a bat, in the 'Flashes Before Your Eyes' time Desmond is on the recieving end.
How do we know that whenever Desmond went back in time, he actually didn't go back? Now that we know that an alternate timeline exists (so to speak), perhaps we can figure out that Desmond's conscious has actually been travelling to the alternate timeline?
Think about it.