I think Hawking has to be on the side of Flocke working on his behalf possibly in both timelines. I think she was given a deal similar to Sayid's, when Flocke promised he could have Nadia back. I think she was told if she worked with him that he would give her her son back and so in the ALT Daniel is alive and well, never pushed to become something he didn't want to become just allowed to become a musician. I think in exchange, Hawking has become in charge of both timelines to keep order. That's why in Flashes before your eyes, she tries to keep Desmond from changing things. That's why she's the one that tells Ben that they all need to go back to the Island including the body of John Locke and that's why she tries to keep Desmond from acting on finding Penny in Happily Ever After. She's be given a role and it is on behalf of the MIB.
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