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The main Navigation screen has nothing to do with how the vehicle starts and runs so the two will not be linked. The issue you have is just with the Nav system or the display it is used on.
Oddly enough something similar recently happened to my 2009 650i recently purchased. The system would intermittently cut out and restart, turning on the radio even with another source selected or radio off. No idea if there is a short or software issue causing it, but it started when I put the navigation DVD in and tried to use it. Took the DVD out and restarted the system, problem hasn’t returned. I’ve read about others having similar issues with the navigation system causing the radio/idrive to cut out as well. It’s a long shot, but worth posting so others don’t spend money chasing a problem solved by using your smartphone instead of the car’s navigation.
I would recomend looking behind the left access cover in the trunk where the navigation computer is located. Inspect the area for any water intrusion, and if possible check the connections to the navigation computer for water or corrossion. the display colors are generated by the navigation computer via RGB lines. If the nav computer is cutting out, that would explain why a battery reset helps restore the picture.
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