Thought I'd share this for others who are upgrading from Drupal 7 to Backdrop.

Sometimes after upgrading the admin menu could have menu items in the wrong place. Usually this is because the menu was probably messed up on your Drupal 7 site. If you're okay with losing the custom menu items in the "management" menu, this is what you need to do to reset it. (Following this thread

I'm going to take the easiest approach for most people. (More experts may want to do this via the CLI).

  1. Backup your database!
  2. Download devel module and install.
  3. Go to Development > Execute PHP (/admin/devel/php).
  4. Then execute the following:
db_query("DELETE FROM {menu_links} WHERE module = 'system'");
db_query("DELETE FROM {menu_links} WHERE menu_name = 'management'");

The admin menu should now be reset and look more normal.