When I open an older file, the dialog appears, I click "Switch" and "Confirm" and then save the file. I then open the file again and no dialog appears anymore. Not even when I restart C4D. I think there must be something special with your files :-(
We will probably be able to fix this, but we would need to see the scene files, which are causing you trouble. You can even remove most of the objects and materials from them, as long as the dialog still appears (the smaller the scene file, the better).