My system now mostly works, but I found some bugs:
All terminal emulator windows are completely transparent. I only know where the windows are because of the shadow effect that Cinnamon casts around them.
The system freezes when I launch the Driver Manager tool.
I have no idea what to do, but it seems that the transition didn't go as smoothly as it should have. On a positive note, my system is now completely silent :)
Update:
I discovered that these issues don't exist with Openbox. Not sure what to make of that.
A complete shot in the dark you might want to see if there are any nvidia dot files laying around and remove them. However, normally switching between Intel and AMD/Nvidia doesnt affect anything so im not sure about the problem.
Make sure you have the packages for OpenGL (hardware acceleration) installed. To make further investigation we need to know which distro you are using :-) There are a lot of Debian distributions with apt...