diff -u b/core/includes/bootstrap.inc b/core/includes/bootstrap.inc
--- b/core/includes/bootstrap.inc
+++ b/core/includes/bootstrap.inc
@@ -217,13 +217,13 @@
   // drupal_static().
   static $files = array();
 
-  // We use drupal static for the bad records so we can test it.
+  // We use drupal static for the missing records so we can test it.
   // Drupal static fast pattern is used as this function may be called often.
   static $drupal_static_fast;
   if (!isset($drupal_static_fast)) {
-    $drupal_static_fast['bad'] = &drupal_static(__FUNCTION__ . ':bad');
+    $drupal_static_fast['missing'] = &drupal_static(__FUNCTION__ . ':missing');
   }
-  $bad = &$drupal_static_fast['bad'];
+  $missing = &$drupal_static_fast['missing'];
 
   // Type 'core' only exists to simplify application-level logic; it always maps
   // to the /core directory, whereas $name is ignored. It is only requested via
@@ -264,16 +264,16 @@
     }
     // If still unknown, perform a filesystem scan.
     if (!isset($files[$type][$name])) {
-      if (is_null($bad)) {
-        $bad = array();
+      if (is_null($missing)) {
+        $missing = array();
         if (\Drupal::hasService('cache.bootstrap')) {
-          $cache = Drupal::cache('bootstrap')->get('drupal_get_filename:bad', TRUE);
+          $cache = \Drupal::cache('bootstrap')->get('drupal_get_filename:missing', TRUE);
           if ($cache && $cache->data) {
-            $bad = $cache->data;
+            $missing = $cache->data;
           }
         }
       }
-      if (!isset($bad[$type][$name])) {
+      if (!isset($missing[$type][$name])) {
         $listing = new ExtensionDiscovery(DRUPAL_ROOT);
         // Prevent an infinite recursion by this legacy function.
         if ($original_type == 'profile') {
@@ -289,11 +289,13 @@
   if (isset($files[$type][$name])) {
     return $files[$type][$name];
   }
-  elseif (!isset($bad[$type][$name])) {
-    // Add the missing file to a temporary cache and throw an alert.
-    $bad[$type][$name] = TRUE;
+  elseif (!isset($missing[$type][$name])) {
+    // Add the missing file to a temporary cache and throw an alert. This cache
+    // will be cleared on cron runs as well as when visiting the module and
+    // theme list pages.
+    $missing[$type][$name] = TRUE;
     if (\Drupal::hasService('cache.bootstrap')) {
-      \Drupal::cache('bootstrap')->set('drupal_get_filename:bad', $bad, REQUEST_TIME);
+      \Drupal::cache('bootstrap')->set('drupal_get_filename:missing', $missing, REQUEST_TIME);
     }
     if (\Drupal::hasService('logger.factory')) {
       \Drupal::logger('system')->error('The following @type is missing from the file system: @name', array('@type' => $type, '@name' => $name));
diff -u b/core/modules/system/src/Tests/Bootstrap/GetFilenameUnitTest.php b/core/modules/system/src/Tests/Bootstrap/GetFilenameUnitTest.php
--- b/core/modules/system/src/Tests/Bootstrap/GetFilenameUnitTest.php
+++ b/core/modules/system/src/Tests/Bootstrap/GetFilenameUnitTest.php
@@ -77,9 +77,9 @@
     $this->assertNull(drupal_get_filename('module', $non_existing_module), 'Searching for an item that does not exist returns NULL.');
 
-    // Get the bad records static from drupal_get_filename.
-    $bad = &drupal_static('drupal_get_filename:bad');
+    // Get the missing records static from drupal_get_filename.
+    $missing = &drupal_static('drupal_get_filename:missing');
 
     // Searching for an item that does not exist creates a static record in drupal_get_filename.
-    $this->assertTrue($bad['module'][$non_existing_module], 'Searching for an item that does not exist creates a static record in drupal_get_filename.');
+    $this->assertTrue($missing['module'][$non_existing_module], 'Searching for an item that does not exist creates a static record in drupal_get_filename.');
   }
 }
only in patch2:
unchanged:
--- a/core/modules/system/src/Controller/SystemController.php
+++ b/core/modules/system/src/Controller/SystemController.php
@@ -186,6 +186,11 @@ public function systemAdminMenuBlockPage() {
    * @todo Move into ThemeController.
    */
   public function themesPage() {
+    //  Clean up the bootstrap "missing files" cache when listing themes.
+    if (\Drupal::hasService('cache.bootstrap')) {
+      \Drupal::cache('bootstrap')->invalidate('drupal_get_filename:missing');
+    }
+
     $config = $this->config('system.theme');
     // Get all available themes.
     $themes = $this->themeHandler->rebuildThemeData();
only in patch2:
unchanged:
--- a/core/modules/system/src/Form/ModulesListForm.php
+++ b/core/modules/system/src/Form/ModulesListForm.php
@@ -174,6 +174,11 @@ public function buildForm(array $form, FormStateInterface $form_state) {
     // Include system.admin.inc so we can use the sort callbacks.
     $this->moduleHandler->loadInclude('system', 'inc', 'system.admin');
 
+    //  Clean up the "missing files" cache when listing modules.
+    if (\Drupal::hasService('cache.bootstrap')) {
+      \Drupal::cache('bootstrap')->invalidate('drupal_get_filename:missing');
+    }
+
     $form['filters'] = array(
       '#type' => 'container',
       '#attributes' => array(
only in patch2:
unchanged:
--- a/core/modules/system/system.module
+++ b/core/modules/system/system.module
@@ -1201,6 +1201,11 @@ function system_cron() {
     $cache_backend->garbageCollection();
   }
 
+  // Clean up the bootstrap "missing files" cache when running cron.
+  if (\Drupal::hasService('cache.bootstrap')) {
+    \Drupal::cache('bootstrap')->invalidate('drupal_get_filename:missing');
+  }
+
   // Clean up the expirable key value database store.
   if (\Drupal::service('keyvalue.expirable.database') instanceof KeyValueDatabaseExpirableFactory) {
     \Drupal::service('keyvalue.expirable.database')->garbageCollection();