I don't know if it messed something up, but I would remove it and clean the inside, not anything under the cover, but make sure the door opens and closes without any catching. Make sure the actual probe thingy isn't damaged while you clean it though. I would see if you can find someone else with a M42 to test their AFM on your car, it's free and could save you a lot of time if that's the issue. Because the ECU tells the AFM when to open and close, manually opening it while it is running could have messed up something mechanically in the AFM.