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No one, including the greatest minds in the world knows what happens during "time travel" since it's all theory. This gives the writers the possiblity to do what ever they want. Right now the only hint that has been dropped on Caitlin's fate is by
Greg Beeman (Director/Producers) who name dropped
Back to the Future 2 as a guide to time travel. In that the lead Marty had to leave his girlfriend Jennifer in an alternate present and go back to the past to change the future. When he returned she was still in the spot he left her while the "future" changed around her leaving her untouched.
As huge time travel nut, even before Greg said this, this was always my assumption, so I never questioned it, I was very surprised when I went online and saw the huge debate.

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Well, that could mean that he'd have to wait until at least the summer of '08 to get her back, or he'd have to time-travel to get there (which if he stick around with Hiro, Hiro would try to prevent him from changing the time continum any more).
Yeah, that's how I saw it.
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And if they kill off another love interest for Peter, what's that make it? 3?
And so is usually the fate of a hero...and James Bond.