diff -u b/includes/bootstrap.inc b/includes/bootstrap.inc
--- b/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -835,7 +835,7 @@
 function drupal_get_filename($type, $name, $filename = NULL) {
   // The location of files will not change during the request, so do not use
   // drupal_static().
-  static $files = array(), $dirs = array();
+  static $files = array(), $dirs = array(), $files_scanned = array();
 
   // Profiles are a special case: they have a fixed location and naming.
   if ($type == 'profile') {
@@ -860,8 +860,13 @@
     try {
       if (function_exists('db_query')) {
         $file = db_query("SELECT filename FROM {system} WHERE name = :name AND type = :type", array(':name' => $name, ':type' => $type))->fetchField();
-        if ($file !== FALSE && file_exists(DRUPAL_ROOT . '/' . $file)) {
-          $files[$type][$name] = $file;
+        if ($file !== FALSE) {
+          if (file_exists(DRUPAL_ROOT . '/' . $file)) {
+            $files[$type][$name] = $file;
+          }
+          else {
+            $database_file_exists = FALSE;
+          }
         }
       }
     }
@@ -894,9 +899,15 @@
         $missing = array();
         try {
           if (function_exists('cache_get')) {
-            $cache = cache_get('drupal_get_filename:missing');
+            $cache = cache_get('drupal_get_filename:missing', 'cache_bootstrap');
             if (!empty($cache->data)) {
-              $missing = $cache->data;
+              // Merge the changes already done in the current request (including
+              // the setting of missing records to NULL) into the values saved
+              // in persistent cache.
+              $missing = $cache->data + $missing;
+              // Set a flag so we know that we've already done a merge with values
+              // in cache_get().
+              $missing['#cache_merge_done'] = TRUE;
             }
           }
         }
@@ -905,6 +916,18 @@
         }
       }
 
+      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.
+          $missing[$type][$name] = NULL;
+          $missing['#write_cache'] = TRUE;
+        }
+      }
+
       if (!isset($dirs[$dir][$extension]) && !isset($missing[$type][$name])) {
         $dirs[$dir][$extension] = TRUE;
         if (!function_exists('drupal_system_listing')) {
@@ -916,7 +939,18 @@
         // called more than once in the same page request.
         $matches = drupal_system_listing("/^" . DRUPAL_PHP_FUNCTION_PATTERN . "\.$extension$/", $dir, 'name', 0);
         foreach ($matches as $matched_name => $file) {
-          $files[$type][$matched_name] = $file->uri;
+          $files_scanned[$type][$matched_name] = $file->uri;
+        }
+      }
+
+      if (isset($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.
+          $missing[$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);
         }
       }
     }
@@ -933,14 +967,30 @@
-      try {
-        if (function_exists('cache_set')) {
-          cache_set('drupal_get_filename:missing', $missing, 'cache');
-        }
-      }
-      catch (Exception $e) {
-        // Hide the error.
-      }
+      $missing['#write_cache'] = TRUE;
     }
     trigger_error(format_string('The following @type is missing from the file system: @name. 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);
   }
 }
 
 /**
+ * Writes the missing and moved files to persistent cache.
+ *
+ * @param array $missing
+ *   The array of missing and moved files.
+ */
+function drupal_missing_write_cache() {
+  if (drupal_get_bootstrap_phase() != DRUPAL_BOOTSTRAP_FULL) {
+    return;
+  }
+  $missing = &drupal_static('drupal_get_filename:missing');
+  if (isset($missing['#write_cache'])) {
+    if (!isset($missing['#cache_merge_done'])) {
+      $cache = cache_get('drupal_get_filename:missing', 'cache_bootstrap');
+      if (isset($cache->data)) {
+        $missing = $cache->data + $missing;
+      }
+    }
+    $missing['#write_cache'] = NULL;
+    cache_set('drupal_get_filename:missing', $missing, 'cache_bootstrap');
+  }
+}
+
+/**
diff -u b/modules/simpletest/tests/bootstrap.test b/modules/simpletest/tests/bootstrap.test
--- b/modules/simpletest/tests/bootstrap.test
+++ b/modules/simpletest/tests/bootstrap.test
@@ -382,7 +382,7 @@
   }
 
   /**
-   * Whether the filename test triggered the right error. 
+   * Whether the filename test triggered the right error.
    *
    * Used by BootstrapGetFilenameTestCase::testDrupalGetFilename().
    *
only in patch2:
unchanged:
--- a/includes/common.inc
+++ b/includes/common.inc
@@ -2751,6 +2751,7 @@ function drupal_page_footer() {
   _registry_check_code(REGISTRY_WRITE_LOOKUP_CACHE);
   drupal_cache_system_paths();
   module_implements_write_cache();
+  drupal_missing_write_cache();
   system_run_automated_cron();
 }