Yes, the audio will work with the nav system removed. However it will do what yours is already doing-- shut off after a couple minutes.

I am thinking that your amp needs recoding. Or your amp simply went bad.

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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