Parallel timelines; one as if the bomb didn't work and one if it did. But what's interesting is that in the second timelines, all the survivors are having problems - Kate is still in custody and now a fugitive, Jin and Sun are being questioned by customs, the airlines lost Jack's father, Charlie got caught with his drugs. Yet, Hurley is having the opposite reaction. Where previously he was all bad luck, now he's the luckiest guy in the world. I think Hurley is a much more central character than we realize and that will come out as the season progresses.
As someone already mentioned, Miles ssid that she said "it worked". Which means she knows something about what's going on.
The only altered part of the reality is what happens after the plane was supposed to crash. Shannon would still be on the plane, but I suspect since they couldn't bring Maggie Grace back, they just ignored her lack of presence. Maybe she was flirting with some guy in coach