In case one changes the CMake configuration settings within the Kit configuration it is added to the .user files of the currently opened project. Removing the configuration settting from the Kit does not update the .user file. So the setting is still applied to the project even it hasn't been ever defined as a project specific cmake configuration but only a Kit specific.
Deleting an entry manually from the project specific CMake settings does not seem to be possible either, so the only way to remove the Kit settings applied before seems to be manually editing the .user file and remove the setting (e.g. CMAKE_CXX_COMPILER_WORKS:STRING=1)