I ran into this as well when my battery died and I replaced it. There is a time out period you can use toget past this. I believe it was in the manual. Essentially you leave the key on for a specific period of time and it bypasses the code. Then it never asks again.

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2013 X5 xDrive3.5i Premium
2002 530I Sport Package
2001 X5 4.4i
2001 M3