Troubleshooting issues with reordering and hiding admin menu items

Complications can arise with menu items that act as main menu items AND submenu items.

For example, the top-level menu item Appearance is actually the same as the sub-menu item Themes. You may find that even though you've hidden all the menus under Appearance, when you drag the Themes item and make it a top level menu, all those hidden sub-menu items will reappear under it.

To remedy this, you'll want to simply rename the Appearance menu item to Themes and simply hide all the rest of the submenu items under it.