Not many are likely to have done this on a new X3 yet, hence the lack of posts. I have had the same experience as Price, no issues on previous models (E46, E53).

You are not sure to have the problem with the panoramic sunroof, the manual warns that it may happen. That is why there is a hand crank in the tool kit, so that you can crank the pano roof closed if you get stuck. I would pull the battery and carry on, taking a chance (but I would have the roof closed when I did it). Worst case is that you have to go to the dealer, but it isn't guaranteed. Good luck, and let un know how it works out.

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2007 X3 3.0si, 6 MT, Premium, White

Retired:
2008 535i, 6 MT, M Sport, Premium, Space Grey
2003 X5 3.0 Steptronic, Premium, Titanium Silver
2002 325xi 5 MT, Steel Grey
2004 Z4 3.0 Premium, Sport, SMG, Maldives Blue