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I selected and ordered Faves items, and the main categories in the left column. Under Settings I've used the Menu utility to hide and show certain things. Looking at it the utility now, under System and Settings there is no Updates item listed, checked or unchecked. Beyond that, I don't recall doing anything that would affect this.
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Do you have a restore point set?
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It looks like he is using the default xfce menu config. Right click on the menu icon and see if it says whisker, if it doesn't this may be the issue. If it still says your using the whisker menu, then try renaming the xfce menu config located in the /home/USER/.config/menus, log out and back in or reboot to see if that fixes.
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Looks like the problem was me not understanding how the Menu configurator is configured. When XFCE is selected on the left, I thought the items on the right were items in the left-hand column of the menu. But they seem to be global filters that will remove the items from the entire menu, including the search function. I restored my menu config file, went into configurator and re-checked Install Updates, which I had disabled. Now Install Updates appeared in a search. From there I added it to Favorites. It still isn't in System though, which I thought it is by default.
So all my questions here have been answered. Thanks again to everyone!