If they replaced the GM they may need to enable one-touch operation, which is a car/key memory option.
Otherwise, the chances that they accidentally disabled the function are EXTREMELY low.
If your owner's manual says to hold the window switch in the auto/full up position and hold it for a while, that is the general initialization procedure.
Either the E46 coupes or convertibles have a revised initialization procedure because the usual wasn't working in certain cases (depending on production date maybe I can't recall). Anyway there was a bulletin, I can paraphrase, but it would be best to find a copy.
My memory of the bulletin:
All doors, trunk, hood, everything needs to be closed. Turn key to second position. It is best to have battery charger hooked up.
1. Bring window to be initialized to top and hold window switch at full up (second detent) for 15s.
2. Lower window 1/3 down.
3. Repeat step 1.
4. Repeat step 2, stop at the same place you stopped last time.
5. Repeat step 1.
6. Repeat step 4.
7. Repeat step 1.
8. Check function of window.
Sounds crazy, I know. Do I think this'll work? Maybe. Give it a shot.