To my surprise, I removed one menu item from the main menu, and it correctly dissapeared from the admin ui, but there still is an entry in the table called menu_links. There is nothing unusual about the entry. How does drupal know it should not be used ? Can I manually remove it ?
The problem is, I use custom code that traverses the menu_links table to generate an alternative menu. This custom code just sees the menu item and keeps on displaying it in the alternative menu. So, is that approach wrong ?