I'm adding onto this thread as I also have the same issue persisting. It seems to be related to a 3.2.x patch as it doesn't appear to happen now that I've reverted to 3.2.0, but I've also noticed I can't modify my indexing setting under the application group in the applications settings, which I thought would be used to control this issue.
Hopefully this gets resolved soon! I manage 3 organizations, and create new projects everyday for various clients. My project folders are getting very long with folders that keep popping up and have nothing but the empty index folder in them.
This issue persists on both local storage and cloud storage drives. I have a network storage that I believe it would occur on too, but the network storage acts as a backup for projects and doesn't have entire projects moving off it very often.