I know this is an old post and is not a feature in Cubase but if there are any Cubase mods around, this is by far my BIGGEST NIGHTMARE when working with configurations. I came here searching for a solution to this exact problem.
I have about 10 different configurations, controlling mix sub groups, returns from a slave machine, and 1000 tracks. It’s a complete nightmare to have to update every single configuration every time I add a reference track or another instrument. It’s probably wasted hours of my time that I could otherwise be using productively.
This could EASILY be solved to everyone’s satisfaction with a little icon to lock the configuration once set.