How do you deploy a change to a main menu? We have a small D7 site. We want to deactivate a main menu item.
On dev server I was able to deactivate it in /admin/structure/menu/manage/main-menu

I believe The menu is stored in the DB, right. Also in a config file? So you only need to deploy those two things and it is done.

Is that correct? If not, what are the steps to deploy a main menu change?
Menu items are saved in the DB, therefore you must update them using update hooks.

Something like this should work:

function MODULE_NAME_update_N() {
  $menu_link_id = 1;
  $menu_link = menu_link_load($menu_link_id);
  $menu_link['hidden'] = 0;
  menu_link_save($menu_link);
}