I am using fedora 30 with xfce. After installation I had two menu entries ‘settings’ and ‘administration’. After using menulibre to add a new menu item those two menu entries are gone. Re-installing redhat-menus did not help.
I fixed that myself after letting my brain some more time. Since menulibre did not ask for admin rights the changes must have been made somewhere in my home. Checked .config and deleted the ‘menus’ folder there. Both menu entries appeared after a new login - problem solved! Just my manual change was gone, but that is just a flesh wound.