when John starts receiving all the new memories, wouldn't everyone else who knew him have the same reaction? It seemed as if only John was the one tripping out, the other two guys acted as if they had already known, even his mother would've called him and tried to figure out what the hell just happened.
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It's because John was the only person who talked to his father and thus the one responsible for altering the course of events. It's like "Back to the Future 2" when Marty and Doc return from 2015 to an alternate 1985 where Biff is in control of everything. Since Marty and Doc were responsible for altering the timeline they remained inside a "bubble" while everything changed around them and everyone else remained oblivious and knew no different. Same deal as "Frequency".
"It looks a bit sweaty in there so you may need to apply baby powder" Zapp Brannigan