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We never saw Ben's full awakening, so we have to assume it happened off-screen with Alex.
Unless we did see it. Perhaps he awoke during that scene in "What They Died For" where he began crying on seeing Alex. We didn't see any flashes, but they might still have come to him.
I'm kind of glad they never showed us Ben's full awakening. It presumably featured Alex, but flash sideways Alex was probably just a figment of his imagination. The emotional scene would have had to end with Ben saying, "Alex! Wait. YOU'RE not Alex. I've been fooled into thinking I was talking to my dead daughter. Again!"
Unless of course sideways Alex actually was real, despite her pigtails and her inexplicable fawning over Ben. That would have turned out even more awkward. If both woke up, Ben would have been saying, "Alex! I love you!" And Alex would have been saying, "Dad! I remember you now. You! I HATE you!"
The closest we got to Ben's awakening were his initial flashes with Desmond. My imagined extension makes the scene only slightly more ridiculous than it really was. Yes, Ben's magical deja vu moment really did consist of him *getting beaten*. A giant gift from the writers to the fans.