One possible direction this may go:
When the woman at the jewelry store in Desmond's flashback was talking about being unable to stop death, it would have been the 3rd time that she would not have been able to save the guy with the shoes. With Desmond/Charlie, Desmond has saved Charlie 2 times now, and now that the 3rd time is approaching, it is making it seem like Charlie will finally die. They seem to be making a big deal out of the number 3 in the cases of trying to save someone's life.
Maybe they will end up raising the significance of Charlie's almost-death in Season 1, and Desmond has actually stopped #2 and #3 of the times when Charlie was supposed to die. This might end up meaning that Desmond really has stopped him from dying.