I can confirm everything you stated in your last post. Then I went a bit farther and found out that the file "user" (with the wrong permissions) will also disappear if I open any application with elevated privileges.
Try this:
Open Nemo normally, without elevated privileges, navigate to .cache/dconf and make sure the file "user" is not present (delete it if you have to).
Open a second instance of Nemo, .cache/dconf with elevated privileges and make sure the "dconf" folder is again empty (it should be).
Set both Nemo windows side bay side so you can view both and refresh Mintupdate. The file "user" should appear in both Nemo windows (with wrong permissions).
Now open a terminal and type:
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sudo -i
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xed
The same thing happened when I started "xplayer", "pix", and "gnome-system-monitor" with elevated privileges via the terminal. Once the file "user" was recreated by refreshing Mintupdate, it would disappear when opening any application with elevated privileges or at least the ones I tried.
By the way, when I got done with all of the above I ran:
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sudo find $HOME ! -user $USER -type f
/home/kmb42vt/.cache/dconf/user
/home/kmb42vt/.config/dconf/user
Both with the wrong permissions obviously. So I ran:
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find /home/$SUDO_USER ! -user $SUDO_USER -exec chown $SUDO_USER:$SUDO_USER '{}' \;
I can duplicate the above consistently as well. As many times as I want to. So if you could confirm this I'd appreciate it and hopefully it may help to isolate what exactly is wrong.