How to disable module warning "User warning: The following module is missing from the file system" only visible on update.php?
Probably you haven't uninstalled the module, so you've to either:


restore the module to its original location and uninstall it,
or manually remove all traces of the module in the database (not recommended) by:


using Module Missing Message Fixer (Drupal 7)
using Drush command:


Drupal 7

drush sql-query "DELETE from system where name = 'old_module1' AND type = 'module';"

Drupal 8

drush sql-query "DELETE FROM key_value WHERE collection='system.schema' AND name='module_name';"


When it's done, clear the site's caches: drush cr.

Or use Devel module by going to: /devel/php and execute:

$query = \Drupal::database()-&gt;delete('key_value')
      -&gt;condition('collection', 'system.schema')
      -&gt;condition('name', 'module_name')
      -&gt;execute();





See: How to fix "The following module is missing from the file system..." warning messages.