Depois de recriar a pasta Documentos, verifique se o ~/.config/user-dirs.dirs
contém algo assim:
XDG_DESKTOP_DIR="$HOME/Desktop"
XDG_DOWNLOAD_DIR="$HOME/Downloads"
XDG_DOCUMENTS_DIR="$HOME/Documents"
XDG_MUSIC_DIR="$HOME/Music"
XDG_PICTURES_DIR="$HOME/Pictures"
XDG_VIDEOS_DIR="$HOME/Videos"
Em seguida, execute o comando xdg-user-dirs-gtk-update
.