We have a content type basic page that has a date field. We use this code in a custom module to delete field collection data in drupal 7.

//Use a query to get all nodes of your particular content type.
 $results = db_query("SELECT nid FROM node WHERE type='your-  content-type'");
$nids = array();
foreach($results as $result)
{
$nids[] = $result->nid;
}
foreach($nids as $nid)
{
//use for loop for testing
$node = node_load($nid);
foreach ($node->field_international_activity[LANGUAGE_NONE]as$key=> $value)
{
// Build array of field collection values.
$field_collection_item_values[] = $value['value'];
// Unset them.  
unset($node->field_international_activity[LANGUAGE_NONE][$key]);
}
// Delete field collection items.
entity_delete_multiple('field_collection_item', $field_collection_item_values);
node_save($node);
}