How to completely wipe and rebuild drupal menus?
I have been looking a while for a solution to the problem to rebuild Drupal menus until I stumbled upon a Drupal issue that helped me. My solution (in a php script) is the following:

db_query("DELETE FROM {menu_links} WHERE module = 'system'");
db_query("DELETE FROM {menu_links} WHERE menu_name = 'management'");
menu_rebuild();


This could also be done by entering the queries through phpmyadmin or something alike:

DELETE FROM {menu_links} WHERE module = 'system'
DELETE FROM {menu_links} WHERE menu_name = 'management'


And then rebuilding the menu structure. If you use the devel module, you can achieve that by visiting the page /devel/menu/reset. I you don't have the devel module, I'm not sure how to rebuild the menu structure.

Don't forget to backup your database before you try this.