Unfortunately you will need to replace the Nav unit. I had the same problem and it took a couple of years
to discover the root of the problem. The bottom line- Nav units installed in 2001 E38s must power down completely before disconnecting the battery.
This takes about 15 minutes. If the battery is disconnected before the unit shuts down, the unit will be damaged and inoperable. BMW issued a service notification on this back in 2002 or 03, can't remember exactly but you can search the net for it. I would suggest browsing Ebay for a replacement, it will cost you about $500 to $600. Good luck.