I got the impression that seeing Charlotte made him remember all of that from the main timeline, much in the same way Desmond remembered things about Penny when confronted with the parallel situation with Charlie in the water. They remember because something in them knows that what they're experiencing in the alternate timeline wasn't supposed to happen, something just has to bring out the part of them that senses that. Which apparently is what Desmond now intends to do to everybody else.
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Like carnivores to carnal pleasures, so were we to desperate measures...
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