Hi, I am using UE 4.9.2, and this problem still exists. The date is 25 Oct 2015 
I created an empty project from FP template (using 4.9.1). Then I changed a few things, added landscape and foliage. I moved two folders containing assets from the root folder to a sub folder. They were successfully “moved”. However, the old folders are still there, “empty”. When I try to delete them I get a message that there are still referenced assets in them. So in effect my assets were not moved, just copied, the old ones were hidden, but their references to the map etc were left in place! What am I supposed to do?