diff -u b/core/includes/common.inc b/core/includes/common.inc
--- b/core/includes/common.inc
+++ b/core/includes/common.inc
@@ -6373,7 +6373,7 @@
   PhpStorageFactory::get('twig')->deleteAll();
 
   // Rebuild module and theme data.
-  $files = system_rebuild_module_data();
+  $module_data = system_rebuild_module_data();
   system_rebuild_theme_data();
 
   // Ensure that all modules that are currently supposed to be enabled are
@@ -6383,6 +6383,12 @@
   // Rebuild and reboot a new kernel.
   // A simple DrupalKernel::reboot() is not sufficient, since the list of
   // enabled modules might have been adjusted above due to changed code.
+  $files = array();
+  foreach ($module_data as $module => $data) {
+    if (isset($data->uri)) {
+      $files[$module] = $data->uri;
+    }
+  }
   drupal_container()->get('kernel')->updateModules(module_list(), $files);
 
   // Update the list of bootstrap modules.