Clion reloads when cmake runs externally

So, it seems that Clion will randomly load the Cmake project when an external build is triggered. Very often it will fail and the indexer is left in a broken state. I will than have to reset the cache and to reload the project. Even when not failing, it slows down the computer, because the external build uses all my cores. This slows down the progress. 

Clion builds into another directory and is not supposed to touch the external build artifacts (different generation path), so how does Clion even notice that? 

I really wish there would be button to disable this "smartness". There is everything fine with the IDE and suddenly: reload and a broken indexer. 

Of course, the checkbox "Automatically reload CMake project on editing" is disabled. 

Help would be appreciated.