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>IANAGU, but what if the user removes a menu item by mistake? Is there any way to undo that?
Yes. All apps that have a proper .desktop file appear in the editor. Next to the name of the app, there's a tick-box. Un-selecting the app in the editor only removes the entry from the users menu. It doesn't remove it from the editor and it doesn't remove the .desktop file.
If the user un-selects the app in the editor, intentionally or by mistake, and, later, wants to return it to his/her menu view, they need only to re-select it in the editor.