Just like the way it is for Make/Ninja Reproducible: Always
This is definitely an inconvenience. Currently switching build tools means wiping the project clean and starting from scratch. Of course doing this in a very robust way is difficult since CMake demands you delete existing build files when switching from one build system to another. It means to do a very nice job would mean saving all the CMake build options and recreating them with Ninja instead of Make. (Or vice versa, if Ninja were somehow giving you problems. I haven't heard of that happening recently though.) A simpler way to do it for the time being would be to allow the user to wipe everything clean and start from scratch using a different build system. They can enter their CMake options again if they have to. (I always write down my configuration options in separate notes files anyway, those variables are too volatile to rely on a separate system to remember them for me.)
@Michael: This bug report is not about switching build tools. It's about being able to modify the environment variables for a given build tool (qmake). Please report your issue in a separate bug.