Programmatically delete a field collection items
function _delete_node_fc_items($node, $field_name) {
$fc_items = field_get_items('node', $node, $field_name);
if (!isset($fc_items[0]))
return;
foreach ($fc_items as $fc_item) {
entity_delete_multiple('field_collection_item', array($fc_item['value']));
}
$node->{$field_name} = array();
node_object_prepare($node);
node_save($node);
}