diff --git a/core/includes/update.inc b/core/includes/update.inc
index b49c9dc26d..a42cc1b6fd 100644
--- a/core/includes/update.inc
+++ b/core/includes/update.inc
@@ -9,6 +9,7 @@
  */
 
 use Drupal\Component\Graph\Graph;
+use Drupal\Core\Extension\Exception\UnknownExtensionException;
 use Drupal\Core\Update\UpdateKernel;
 use Drupal\Core\Utility\Error;
 
@@ -29,7 +30,13 @@ function update_fix_compatibility() {
   $save = FALSE;
   foreach (['module', 'theme'] as $type) {
     foreach ($extension_config->get($type) as $name => $weight) {
-      if (update_check_incompatibility($name, $type)) {
+      try {
+        $is_incompatible_or_missing = update_check_incompatibility($name, $type);
+      }
+      catch (UnknownExtensionException $exception) {
+        $is_incompatible_or_missing = TRUE;
+      }
+      if ($is_incompatible_or_missing) {
         $extension_config->clear("$type.$name");
         $save = TRUE;
       }
@@ -295,9 +302,11 @@ function update_get_update_list() {
   $ret = ['system' => []];
 
   $modules = drupal_get_installed_schema_version(NULL, FALSE, TRUE);
+  /** @var \Drupal\Core\Extension\ExtensionList $extension_list */
+  $extension_list = \Drupal::service('extension.list.module');
   foreach ($modules as $module => $schema_version) {
     // Skip uninstalled and incompatible modules.
-    if ($schema_version == SCHEMA_UNINSTALLED || \Drupal::service('extension.list.module')->checkIncompatibility($module)) {
+    if ($schema_version == SCHEMA_UNINSTALLED || $extension_list->checkIncompatibility($module)) {
       continue;
     }
     // Display a requirements error if the user somehow has a schema version