I remember there was an option to modify the 3D version (e.g. move a machine) while keeping frozen the 2D version.
Could you please remind me how to do this?
I guess you are talking about changing object positions in 2D and 3D independently from each other.
The flag you are searching is the Connect 2D<>2D flag which you can find in the 3D properties dialog of the respective object on the transformation page.
However, I would recommend to take a minute or two to think about alternatives because, in my experience, models tend to become pretty chaotic after some time because more and more the layouts starts to differ (this all depends on the user, of course, but that is my general impression).