You can use OS.get_ticks_msec(), which gives the elapsed time since the engine started. Just save it with your objects and check the difference when they're loaded.
Doing what you say is pretty questionable though. Running their physics process to make up for lost time defeats the point of saving them in the first place, extrapolating from their last velocity sounds okay even though it won't take into account collisions, but that could easily take them out of their sector. If you're just dealing with asteroids, you might want to just reposition them randomly. Though you'd probably still want to check the time and only do that if a certain amount of time has passed.
