user-dirs.dirs reset at start-up

I wanted to have some of the sub-folders of my home directory (like Music, Downloads,Videos) on my hard-disk-raid instead of my SSD. Therefore I deleted those folders in my home directory, recreated them on the RAID and made symlinks pointing from my home-folder to the RAID (e.g. /home/user/Music > /mnt/home-big-data/user/Music). However, the newly created folders don't have the correct meta-data-properties in Gnome 3 (wrong icon, folders won't open as Music folder, etc.). Which is the best way to remap those features to the folders on the RAID? I tried editing the /home/user/.config/user-dirs.dirs and setting XDG_DOWNLOAD_DIR="$HOME/Downloads" (according to the symlink) but it was resetted to XDG_DOWNLOAD_DIR="$HOME/" after reboot. Another thing I tried was using gvfs-set-attribute to reset the standard-icon, but this also failed. Which would be the correct way to do that?