Script to help cleanup the non existing permissions from your roles

See: https://www.drupal.org/node/3193348#comment-14969643

web]$ ../vendor/drush/drush/drush php-script ../drush-scripts/clean_permissions.php

<?php
/**
 * @file
 * Script to help cleanup the non existing permissions from your roles.
 *
 * @code
 * drush scr clean_permissions.php
 * drush -y cex
 * @endcode
 *
 * @see https://www.drupal.org/node/3193348
 */
$entity_type_manager = \Drupal::entityTypeManager();
$permissions = array_keys(\Drupal::service('user.permissions')->getPermissions());
/** @var \Drupal\user\RoleInterface[] $roles */
$roles = $entity_type_manager->getStorage('user_role')->loadMultiple();
foreach ($roles as $role) {
  $role_permissions = $role->getPermissions();
  $differences = array_diff($role_permissions, $permissions);
  if ($differences) {
    foreach ($differences as $permission) {
      $role->revokePermission($permission);
    }
    $role->save();
  }
}