I have a 1996 SL500. In my car when battery disconnets, to resync. the windows I do this: Just close the door with window down+After door is closed push the button to raise the window+when window reaches the top hold the button pushed another 2-3 seconds.
That should do it. Repeat for the other window. Then when you re-open the door, window comes down a little automatically to show that it's resync'd.