When i delete some folders in content browser, they appear again next time i run the project. Everytime i delete them they appear again.
When i rename some folder with lot of things in it (few giga) the editor stops working for like 20 minutes or more.
I have come across this in the past as well.
Sometimes deleting folders in the content browser doesn’t remove them completely.
The additional step you need to take is to go to your content folder and manually delete it.
I haven’t had this problem since moving to UE 4.14 so I believe it has been fixed.