UserCleanup.php

<?php

$users = \Drupal::entityQuery('user')
  ->execute();

$max = count($users);
$pointer = 0;
foreach (array_chunk($users, 100) as $chunk) {
  foreach ($chunk as $user_id) {
    $pointer++;
    $user = \Drupal\user\Entity\User::load($user_id);
    foreach ($user->getFieldDefinitions() as $key => $field) {
      if (!$field instanceof \Drupal\field\Entity\FieldConfig) {
        // Not interested in base fields.
        continue;
      }
      if ($field->getType() != 'entity_reference') {
        continue;
      }
      $need_repair = FALSE;
      $valid_keys = [];
      $invalid_keys = [];
      foreach ($user->get($key) as $key_field) {
        if (!$key_field->entity) {
          // Missing entity. Update this field from this contact.
          $need_repair = TRUE;
          $invalid_key = $key_field->target_id;
          $invalid_keys[$invalid_key] = $invalid_key;
          continue;
        }
        $valid_key = $key_field->target_id;
        $valid_keys[$valid_key] = $valid_key;
      }
      if ($need_repair) {
        $string = implode(" ,", $invalid_keys);
        drush_print("Removed references to IDs {$string} from user {$user_id} field {$key}");
        //$user->set($key, $valid_keys);
        //$user->save();
      }
    }
  }

  $status = floor($pointer / $max * 100);
  drush_print("Processed $status%");
}