diff -u b/includes/bootstrap.inc b/includes/bootstrap.inc
--- b/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -910,6 +910,18 @@
         }
       }
 
+      if (isset($missing[$type][$name]) && is_string($missing[$type][$name])) {
+        // This file has moved and the result of a file scan had been cached.
+        if (file_exists($missing[$type][$name])) {
+          $files[$type][$name] = $missing[$type][$name];
+        }
+        else {
+          // File is not available anymore at its new location. Re-do file scan.
+          unset($missing[$type][$name]);
+          $missing['#write_cache'] = TRUE;
+        }
+      }
+
       if (!isset($dirs[$dir][$extension]) && !isset($missing[$type][$name])) {
         $dirs[$dir][$extension] = TRUE;
         if (!function_exists('drupal_system_listing')) {
@@ -928,7 +940,8 @@
       if (isset($files_scanned[$type][$name])) {
         $files[$type][$name] = $files_scanned[$type][$name];
         if (isset($database_file_exists) && $database_file_exists === FALSE) {
-          // This file has moved. Cache its new location into the missing files cache.
+          // This file has moved. Cache its new location into the missing files
+          // cache.
           $missing[$type][$name] = $files_scanned[$type][$name];
           $missing['#write_cache'] = TRUE;
           trigger_error(format_string('The following @type has moved on the file system: @name. Clearing caches may help fix this. For more information, see <a href="@documentation">the documentation page</a>.', array('@type' => $type, '@name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
@@ -2526,7 +2539,8 @@
   spl_autoload_register('drupal_autoload_interface');
 
   // Reset the drupal_get_filename() static missing filenames cache as it
-  // may have previously been initialized without the database being available.
+  // may have previously been initialized without the database being
+  // available.
   drupal_static_reset('drupal_get_filename:missing'); 
 }