Embedded field collection not saving with node using conditional fields
I think, it's because field collection is not part of the node, field collection is a separate entity, which needs to be saved separately. 

I once had to add up some number fields and save the value in a field collection field on hook_node_presave

/**
 * Implements hook_node_presave().
 */
function MYMODULE_node_presave($node)
{
  foreach ($node-&gt;field_collection_field[LANGUAGE_NONE] as $key =&gt; $value) {
    $fc_id = $node-&gt;field_collection_field[LANGUAGE_NONE][$key]['value'];
    $field_collection_item = entity_load_single('field_collection_item', $fc_id);
    $field_collection_item-&gt;save(TRUE);
  }
}