Let's say we add the following in Kit's CMake configuration:

CMAKE_TOOLCHAIN_FILE:STRING=/home/foo/bar/Toolchain-v1.8.0.cmake

Then this is passed to CMake as expected. However, when changing (possibly after a restart of Qt Creator, such that it has written its CMakeList.txt.user file before the change) to e.g.

CMAKE_TOOLCHAIN_FILE:STRING=/home/foo/bar/Toolchain-v2.0.0.cmake

the new Toolchain file is not picked up. Only after changing the variable in CMakeList.txt.user does Qt Creator pick it up correctly. So it seems that CMakeList.txt.user has priority over the Kit's CMake configuration, which comes as a surprise.