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Well, during his flashes to 2004, he is confused and disoriented. Until he's told to find Farady, he thinks they're dreams.
The only people he sees are Sayid, who he doesn't recognize obviously, and the doctor/patient on the boat.
So it's not like he'd know they had any connection to the island until after the entire episode in 2004.
He probably remembers the 1996 flashes and going to see Faraday, but chalks it up as a confusing/strange episode in his life 8 years earlier that had no correlation to the events on the island.
Until afterwards.
The only thing is he knows he will call Penny 8 years later, so he would remember that was coming up. Or not. 8 years is a long time and he probably moved on from the whole episode.
I don't really keep in mind any strange dreams or episodes that happened to me 8 years ago.
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