That might be a tough case, but it will depend on your relationship with the dealership. The CPO warranty classifies the nav computer as an "accessory," and the CPO does not cover accessory components. I was pretty ticked when I first learned this. (Essentially, an accessory is just about any electrical item not essential for vehicle operation.)

You could try another operating system downgrade and upgrade to see if that kick starts it back to life. If not, the worst case scenario is that you could end up buying a used MKIV from somewhere like eBay for about $750. They are easy to change out yourself, and that would save you a couple grand.

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SOLD
2000 E38 750iL Highline Edition, Upgraded with the lastest 2006 X5 Electronics
MKIV Navigation, 16:9 Display, Bluetooth, TV/Video with Backup Camera, Sirius, and Aux Input