Ahh, finally I have discovered a workaround. This command, executed in a TTY (which I can access with ctrl-alt-F5 or similar), seems to gently restart gnome-shell and give me everything back with my applications all still running:
dbus-send --type=method_call --print-reply --dest=org.gnome.Shell /org/gnome/Shell org.gnome.Shell.Eval string:'global.reexec_self()' -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1181666 Title: gnome-shell randomly blocks mouse clicks from working in app windows To manage notifications about this bug go to: https://bugs.launchpad.net/gnome-shell/+bug/1181666/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs