I use IntelliJ and Clion daily and I have never noticed any sort of instability.
I used to experience long indexing times until I learned that I chronically misconfigured projects and included build and autogenerated dirs in the index, which is trivially solved by excluding them and invalidating the cache. We're talking about something you do once right after you import the project.
The only foobared filesystem issue I ever stumbled upon was when I toyed with junctions pointing to a RAM drive on Windows, and Clion left the junctions out of the project view.
And that was it.
Could you please elaborate and point out real world examples that showcase any instability you implied?