Comment 129 for bug 260492

Oh yeah -- if you do have older .desktop files, created by nautilus, in ~/.local/share/applications, you can still have the Trash opened with the movie player, etc. I had to delete those, specifically an old version of nautilus-folder-handler.desktop.

So the problem with this affecting upgrading users, rather than new installs, remains. That might be a wishlist bug for nautilus itself, for newer versions to clean up those old files. That might be more likely than trying to do it through update-manager.