Theory:
Time hasn't progressed between portal 1 and 2... relative to the rest of the world.
The combine created a very slow teleporter, what happens if the entire research facility up and went just like the Borealis's drydock, the difference being that when it teleported through space, even if it was only a few feet, it would appear in the future, but in a reverse time dilation thing so that instead of an instantaneous transit from view of the facility, its instantaneous from the rest of the world?
Sort of like stopping time I suppose.
Jus' sayin.