having the same problem on my E46
when I see no CD option I shut the car and restart it again then the CD option is back
Tom from EAS told me that I have to disconnect the battery and do some procedures but I didn't.. Here is what he said:

1. Disconnect iPod from cable
2. Remove battery cables, negative first
3. Touch battery cable terminals together (away from battery) for +5 seconds, a small spark is normal as this is stored power draining from the system.
4. Allow cables to remain disconnected for about 5-7 minutes
5. Reconnect battery cables onto battery, negative last.
6. Reboot iPod by pressing on MENU and CENTER buttons for +5 seconds and then reconnecting to the DICE cable after the reboot process is completed.

__________________
BMW 1M 2012 - Current
Jeep Grand Cherokee Limited 2011 - Current
BMW E93 330i Convertible 2009 - Sold
BMW E46 320i 2004 - Sold
BMW X5 4.4i 2002 - Sold
VW Golf GTI 2000 - Sold
BMW 740i 1996 - Sold