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 https://drupal.stackexchange.com/questions/48515/how-to-completely-wipe-and-rebuild-drupal-menus).

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. https://backdropcms.org/project/devel
  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'");
menu_rebuild();

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