I use to have the option of closing your windows and sunroof from outside the car by putting the key in the door, turning and holding. When I did my stereo last year, disconnected the battery first, I ran the wires thru the factory wireloom between the door. Everything was completed and re connected the battery. A few days later I noticed, I went to put my windows up in a hurry...to my surprise it didnt work. Could it be something that lost programming or something?? I miss this luxury.

 

When you disconnected the battery, they most likely lost the timing for the auto functions.

I do not know the exact procedure for Mini, sorry, but it should be like other makes.

For the windows, try putting them in the full upright position, then with the doors closed lower them with the switch manually (don't do auto down) till it is all the way down then hold the switch in the down position for a few seconds. Then do the same thing going up with the window, hold it for a few seconds after it gets to the full up position.
The same procedure with the sunroof, fully open then close.

Sorry if it does not work, it is how a lot of Japanese made models do the programming. Doesn't hurt to try though. Let me know if it worked, want to know for my reference if I am right or not.

 

nope...that didnt work. I just tried it tonight, in the rain

 

Now we know...and knowing is half the battle.