She's smart and knows a lot about the island. She's also the only one who knew about the time travelers in the 70s (I think). She at least knows that her son somehow makes it to the island and comes back to the 70s where she shoots him. Since the island is gone and that can't happen now, she probably put two and two together. In fact if anyone in the flash sideways world knew what was going on, it would be her.

This was a great episode and it finally moved the flash sideways plot along. It also helped that some of the more interesting and likeable characters (Desmond, Charlie, Daniel) were featured. It was the first episode of the season where I wanted to see more right after it ended. Desmond's flash sideways storyline has turned out to be the only interesting and relevant one so it sucks that his turn is over already (hopefully he'll get a lot more screentime in the final episodes because he seems to be the key to everything). Really I wish it hadn't taken a bunch of crap filler episodes to get to this point but oh well I hope we're in end game now.