Entity Update Failing: How can I clean this up?
Update: it seems that you need to run cron to complete the field purging process drupal goes through.

Also you may be getting some errors when the fields you are deleting have data in them . entup does not attemp to drop fields with data in them and you have to do it yourself. You have 2 options: 


Go to each field in the content type and delete them manually.
Write an update hook that delete the fields before you run entup. In other words, you run drush updb then you run drush entup provided you have implemented an update hook that deletes the fields. Something like this (code not tested): 

function my_module_update_8001() {
   $entity_type = 'node'; // or user or wherever the field appears
   $bundle_name = "article"; // or whereever the field appears
   $field_machine_names = array('field_one', 'field_two');
   foreach($field_machine_names as $field_machine_name) {
    $field = \Drupal::entityManager()-&gt;getStorage('field_config')-&gt;load($entity_type.$bundle_name.$field_machine_name);
    $field-&gt;delete();

  }
}



In addition, make sure that you run cron frequently because that's when drupal does garbage collection and deleted field data get purged.