=== modified file 'includes/menu.inc'
--- includes/menu.inc	2007-12-06 09:58:30 +0000
+++ includes/menu.inc	2007-12-06 19:45:41 +0000
@@ -1598,11 +1598,13 @@ function _menu_navigation_links_rebuild(
       }
     }
   }
-  $result = db_query("SELECT ml.link_path, ml.mlid, ml.router_path FROM {menu_links} ml WHERE ml.updated = 1");
+  $result = db_query("SELECT ml.link_path, ml.mlid, ml.router_path, ml.updated FROM {menu_links} ml WHERE ml.updated = 1");
   while ($item = db_fetch_array($result)) {
     $router_path = _menu_find_router_path($menu, $item['link_path']);
-    if (!empty($router_path) && $router_path != $item['router_path']) {
-      db_query("UPDATE {menu_links} SET router_path = '%s' WHERE mlid = %d", $router_path, $item['mlid']);
+    if (!empty($router_path) && ($router_path != $item['router_path'] || $item['updated'])) {
+      // If the router path and the link path matches, it's surely a working
+      // item, so we clear the updated flag.
+      db_query("UPDATE {menu_links} SET router_path = '%s', updated = %d WHERE mlid = %d", $router_path, $router_path != $item['link_path'], $item['mlid']);
     }
   }
 }
@@ -1631,9 +1633,9 @@ function menu_link_delete($mlid, $path =
  * Helper function for menu_link_delete; deletes a single menu link.
  */
 function _menu_delete_item($item) {
-  // System-created items are never deleted.
-  if ($item && ($item['module'] != 'system')) {
-
+  // System-created items are never deleted. Updated items are an exception,
+  // as they can be broken.
+  if ($item && ($item['module'] != 'system' || $item['updated'])) {
     // Children get re-attached to the item's parent.
     if ($item['has_children']) {
       $result = db_query("SELECT mlid FROM {menu_links} WHERE plid = %d", $item['mlid']);

=== modified file 'modules/menu/menu.admin.inc'
--- modules/menu/menu.admin.inc	2007-12-06 10:37:47 +0000
+++ modules/menu/menu.admin.inc	2007-12-06 17:53:02 +0000
@@ -95,7 +95,7 @@ function _menu_overview_tree_form($tree)
       $operations = array();
       $operations['edit'] = l(t('edit'), 'admin/build/menu/item/'. $item['mlid'] .'/edit');
       // Only items created by the menu module can be deleted.
-      if ($item['module'] == 'menu') {
+      if ($item['module'] == 'menu' || $item['updated'] == 1) {
         $operations['delete'] = l(t('delete'), 'admin/build/menu/item/'. $item['mlid'] .'/delete');
       }
       // Set the reset column.
@@ -534,8 +534,9 @@ function menu_edit_menu_submit($form, &$
  * Menu callback; Check access and present a confirm form for deleting a menu link.
  */
 function menu_item_delete_page($item) {
-  // Links defined via hook_menu may not be deleted.
-  if ($item['module'] == 'system') {
+  // Links defined via hook_menu may not be deleted. Updated items are an
+  // exception, as they can be broken.
+  if ($item['module'] == 'system' && !$item['updated']) {
     drupal_access_denied();
     return;
   }

=== modified file 'modules/system/system.install'
--- modules/system/system.install	2007-12-04 16:39:22 +0000
+++ modules/system/system.install	2007-12-06 19:56:42 +0000
@@ -2327,11 +2327,6 @@ function system_update_6021() {
   }
 
   if ($_SESSION['system_update_6021'] >= $_SESSION['system_update_6021_max']) {
-    $result = db_query('SELECT * FROM {menu_links} WHERE updated = 1 AND has_children = 0 AND customized = 0 ORDER BY depth DESC');
-    // Remove all items that are not customized.
-    while ($item = db_fetch_array($result)) {
-      _menu_delete_item($item, TRUE);
-    }
     if (!empty($_SESSION['menu_bogus_menus'])) {
       // Remove entries in bogus menus. This is secure because we deleted
       // every non-alpanumeric character from the menu name.