Remove original audio & now diagnostic tool cannot be used

[gravedilute]

2007 X3.

I've removed the original audio (Business CD) and replaced with a Kenwood flip-out, rear camera, bluetooth and nav. All good except today when I took it to the dealer as I wanted to change the settings e.g door lock to auto and a couple of other adjustments.
The service fault finder picked up that there were changes to the system, obviously, radio, camera etc. In short they were unable to use the diagnostic fault finder and will not be able to use this tool in the future on the car due to the changes.

Any suggestions? I'm thinking unplug the new head unit and plug the old unit back in but what would be the cause of this?