Some of that stuff uses fiber optic wire. On my car it is a green colored wire. Fiber optics use continuous loops, and if the loop is broken then communication is broken. Termination loops are used to replace components in fiber optic systems keep the loop continuous. Another way is to trace the sources of the fiber optic connected components you want to keep and use the existing fiber optic wire to make/retain those connections; there is a fiber optic bridge in the drivers side rear seat under the cushion at the seat belt that connects the rear amp and rear control modules to everything up front. Changing the paths of these fiber optics can allow components to be removed while maintaining the continuous loop. There is a lot of info on this subject on e90post. This may not be what is happening with you, but it's the first thing that came to my mind when I read what you disconnected.
Part of this process would be to check for fault codes and do coding for things permanently removed.
When I removed the satellite radio component in the trunk I used this 7-series termination loop and connector:
https://www.fcpeuro.com/products/bmw...0group%20%231v
https://www.fcpeuro.com/products/bmw...ng-61136917978