Answer:
When creating user-defined toolbars, you should always ensure that no commands are moved to the standard toolbars and menus. During the installation after updates, the predefined toolbars are always overwritten by the custom toolbars. The user-defined toolbars and menus are compatible and remain after upgrades as well.
In the "Configuration Manager" dialog box, you can use the "Export Configuration as File" option to save the entire setting, including all other objects (colors, options, borders, and so on).