IMO, take the $2000 and make sure that the windshield replacement is not somehow part of the sale paperwork, ie the window change is completed and is not done after you take possession. You want the same vehicle warranty as if the windshield had not been replaced. With that, there is very little risk. A high percentage of new vehicles have repairs, etc, without the owner ever knowing. Why is the post-manufacturing glass installation so different than the installation done in the factory?

The discount seems fair to me.

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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