I remember I deleted a built-in directory like "Documents", and it lost its custom document icon, even when I created a "Documents" directory anew. No amount of googling / asking forums and IRC could bring my custom icon back. :)
If you delete one folder the file $HOME/.config/user-dirs.dirs will be updated sooner or later, and point to $HOME/ and the icon will not be restored by recreating any folder.
(Linux Mint, Cinnamon)