To reproduce:
1. Install / Generate a class that declares a root-level MenuItem. Example: Asset Store Tools (https://www.assetstore.unity3d.com/#/content/115)
2. Once installed and the root level menu item is visible (menu "Asset Store Tools" if following example), delete the class that declares the menu item and wait for recompile
3. Switch away from Unity and back.

Expected result:
Deleting a class that declares MenuItem updates the menu to remove the declared menu item, whether it is root-level or not.

Actual result:
Create root level menu item is always visible even though the class declaring it no longer exists, and obviously clicking it does nothing.

Broken root-level MenuItem persists until restarting Unity or opening another project.