=== modified file 'modules/system.module'
--- modules/system.module	
+++ modules/system.module	
@@ -901,6 +901,10 @@ function system_modules() {
   ksort($files);
 
   foreach ($files as $filename => $file) {
+    if (!drupal_get_filename('module', $file->name)) { // file doesn't exist - we need to update the database
+      watchdog('file system', t('%module has moved to %newfile. System settings changed accordingly', array('%module' => $file->name, '%newfile' => $file->filename)));
+      db_query("UPDATE {system} SET filename = '%s' WHERE name = '%s'", $file->filename, $file->name);
+    }
     drupal_get_filename('module', $file->name, $file->filename);
     drupal_load('module', $file->name);