How do you deploy a change to a main menu?
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);
}