For some reasons, when an XDG user directory (i.e., Desktop, Downloads, Templates, Public, Documents, Music, Pictures, or Videos) is empty, it turns into a symbolic link after some time. Below is an example when it happens to Downloads.
toto@pc-toto:~$ ls -l
total 60K
drwxrwxr-x 3 toto toto 4.0K Aug 31 10:10 Desktop/
drwxr-xr-x 5 toto toto 4.0K Aug 11 13:52 Documents/
lrwxrwxrwx 1 toto toto 21 Aug 31 10:51 Downloads -> /home/toto/Downloads
drwxr-xr-x 7 toto toto 4.0K Aug 3 16:50 Music/
drwxr-xr-x 26 toto toto 4.0K Aug 3 16:53 Pictures/
drwx------ 11 toto toto 4.0K Aug 9 11:34 snap/
drwxr-xr-x 5 toto toto 4.0K Aug 3 16:55 Videos/
toto@pc-toto:~$
This started to happen a few days ago on Ubuntu 23.04. It has also been seen on Ubuntu 20.04: Home directories turned into symbolic links without telling me the reason.
The empty folders will turn into symbolic links in a matter of hours. I didn't find any reason for this.
EDIT: The problem is still going on after upgrading to Ubuntu 23.10.
Temporary solution
Delete the symbolic link and recreate the relevant directories.
toto@pc-toto:~$ rm Downloads
rm: remove symbolic link 'Downloads'? y
toto@pc-toto:~$ mkdir Downloads
toto@pc-toto:~$ ls -l
total 64K
drwxrwxr-x 3 toto toto 4.0K Aug 31 10:10 Desktop/
drwxr-xr-x 5 toto toto 4.0K Aug 11 13:52 Documents/
drwxr-xr-x 2 toto toto 4.0K Aug 31 10:51 Downloads/
drwxr-xr-x 7 toto toto 4.0K Aug 3 16:50 Music/
drwxr-xr-x 26 toto toto 4.0K Aug 3 16:53 Pictures/
drwx------ 11 toto toto 4.0K Aug 9 11:34 snap/
drwxr-xr-x 5 toto toto 4.0K Aug 3 16:55 Videos/
toto@pc-toto:~$
Then, add a hidden file in each directories. This would prevent the directories to become empty and to turn into symbolic links.
toto@pc-toto:~$ cd Downloads
toto@pc-toto:~/Downloads$ touch .empty_file
toto@pc-toto:~/Downloads$
Finally, edit the file ~/.config/user-dirs.dirs to put the right paths of XDG directories back. For example, replace XDG_DOWNLOAD_DIR="$HOME/" by XDG_DOWNLOAD_DIR="$HOME/Downloads".
Note: Since the appearance of the symbolic links, this file won't be affected until you reboot.
