Apparently, importing ~/.config/kglobalshortcutsrc is enough for the shortcut to show up in the System Settings, but not enough to load the shortcut. Disabling, applying and re-enabling and applying again also doesn’t help, and neither does re-assigning to the same shortcut, which resulted in this lovely error dialog.
Although I’m not sure about that, my first reaction to the super key, not working would be to press other keys like control our alt