Why do deleted Content Browser folders reappear?

It’s pretty difficult to keep a project slim and clean if you have to fight against those anoying zombie-folders. Is it save to delete your folders in windows-explorer? Or does it mess up other (redirection) stuff if you do that? Sometimes I don’t really know anymore what’s there and what just looks empty. For example if an fbx import failed for some reason, and you fix fbx and reimport to the “empty” folder than you could crash UE4 editor.