The whole suspension is moved downward- lower control arms, spindles, upper control arms, etc. They all move in unison. I guess since that minimal 2" lift keeps the suspension still well within it's normal range of motion, the computer is fine with it. At the same time, I added 1" coil spacers to the rear, so at least the front and rear were changed somewhat proportionately, so the computer wouldn't see it as a sagging rear.
If I had a Tech2, I certainly would've reset the ride height positions and then again when I removed the lift.