How to make permanent change to .config/user-dirs.dirs?

Each time I changed and saved .config/user-dirs.dirs, and after restarted the system, the XDG_DOWNLOAD_DIR are reverted:

diff --git a/.config/user-dirs.dirs b/.config/user-dirs.dirs
index 8f6e2db..dcff34e 100644
--- a/.config/user-dirs.dirs
+++ b/.config/user-dirs.dirs
@@ -7,11 +7,9 @@
 # 
 XDG_PUBLICSHARE_DIR="$HOME/public"
 XDG_TEMPLATES_DIR="$HOME/public/template"
-
 XDG_DESKTOP_DIR="$HOME/private/desktop"
 XDG_DOCUMENTS_DIR="$HOME/private/doc"
 XDG_PICTURES_DIR="$HOME/private/picture"
 XDG_MUSIC_DIR="$HOME/private/music"
 XDG_VIDEOS_DIR="$HOME/private/video"
-
-XDG_DOWNLOAD_DIR="$HOME/var/downloads"
+XDG_DOWNLOAD_DIR="$HOME/"

How to make my changes permanent?

I think this is the proper way to do it:

xdg-user-dirs-update --set DOWNLOAD $HOME/var/downloads

See xdg-user-dirs in Ubuntu Software Center:

It sets up a config file in $(XDG_CONFIG_HOME)/user-dirs.dirs. Change the default directories and their initial values in /etc/xdg/user-dirs.defaults. The values are relative pathnames from the home directory.