So, although it’s not a fix to engine itself, I’ve found a way to permanently delete folders/content from content browser so we can all avoid that clutter. Open up your project folder wherever it’s located on your PC, mine is in my documents folder within file explorer. Go into your content folder within your project and adjust your folders from within there. Deleted folders will stay deleted, moved folders will remain moved to their new locations without duplicating folders, etc… I’ve tested on engines 4.11 - 4.14, this method works on them all. I don’t know if anyone else has been doing this, but I didn’t see it posted as a solution, even if it is just a temporary solution until engine is fixed.
Again, it’s not a fix to engine itself, it’s just a “desktop fix” that will help maintain that clutter within your project. Hope this helps.