This may be related to this bug or possibly a separate bug. I can re-
file this comment if necessary. I have created a script in the
/etc/X11/Xsession.d folder that is numbered to run *before* the xdg-
user-dirs-update script. My script detects whether or not the Desktop
and Documents folders have been replaced with an appropriate folder
symbolic link of the same name and if it they haven't then it replaces
them. However, the user-dirs-update script apparently "detects" that the
actual folders have been replaced and forces nautilus to use the $HOME
folder in ~/.config/user-dirs.dirs for both of them instead of the
appropriate symlink. The strange part is it will only complain that they
have been replaced with symlinks if xdg-user-dirs-update is run from
within a script or sourced, but it will actually give the correct
folders if it is run directly from the command-line. If it is run from
the command-line it will *not* update the user-dirs.dirs file but if I
delete the user-dirs.dirs file completely it will replace it and if it
is sourced or run within the script then it does actually seem to update
the user-dirs.dirs file though with $HOME instead of the correct
folders.

-- 
A misplaced ~/Templates folder over a reboot permanently changes the TEMPLATES 
path in ~/.config/user-dirs.dirs
https://bugs.launchpad.net/bugs/285998
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