re-saving users with default field collection items
This finally worked for me -- may it save someone hours of headaches:

// load the user
$userwrapper = entity_metadata_wrapper('user', $entity);
// apparently you have to create the field collection entity
$fieldCollection = entity_create('field_collection_item', array('field_name' =&gt; 'field_yourCollectionName'));
// attach your field collection to the user
$fieldCollection-&gt;setHostEntity('user', $entity);
// set the value of one of your fields in your field collection - in my case it's a boolean
$userwrapper-&gt;get('field_yourCollectionName')-&gt;field_fieldNameInYourCollection-&gt;set(0);
// save the entity
$userwrapper-&gt;save();