Somehow my Mate desktop got corrupted. It initially had only the home and trash folders. Now it shows all the files and folders in my /home/username folder. If I go into MATE Tweak and uncheck "Show Desktop Icons", all the files and folders disappear. This is not exactly what I want. I would like for my desktop to only show the items I have checked in MATE Tweak.
@ugnvs in the dconf editor the desktop-is-home-dir flag is off. If I toggle it, nothing happens. I still get all the files and folders appearing on my desktop.
I have had some strange things happen when changing from one panel layout to another in Tweak. Sometimes I've had things break. Sometimes, quirky behavior has "fixed" itself when switching back to the default layout and then to my preferred one, and vice versa. I'm on 18.04, though, so this might be different for you.
Maybe if you play with those a bit you might get it back. Not a satisfying answer. You shouldn't have to reboot to check--at most a log out/in would be sufficient.