This codeigniter script helped me to migrate koha's biblioitems.marcxml into biblio_metadata table after upgrading. To use it, set up codeigniter and configure it to connect to the old koha database and the new database. Then include this class in controllers. Run it via the commandline.

Migrate.php

<?php defined('BASEPATH') OR exit('No direct script access allowed');

class Migrate extends CI_Controller {

        public function __construct(){

        parent::__construct();

        $db = &get_instance();
        $this->db = $db->load->database('default', TRUE);


        $old_koha = &get_instance();
        $this->old_koha = $old_koha->load->database('old_koha', TRUE);

    }

    public function migrate_marcxml(){

		$q = $this->old_koha->query("SELECT biblionumber, timestamp, marcxml FROM biblioitems");

        $success = 0;
        $fails = 0;


		foreach ($q->result() as $row){
			echo "\nMigrating biblio ".$row->biblionumber;
			if (!$row->marcxml){$marcxml = "";}else{$marcxml = $row->marcxml;}

			$data = array(
				'biblionumber'=>$row->biblionumber,
				'metadata'=>$marcxml,
				'timestamp'=>$row->timestamp,
				'format'=>'marcxml',
				'marcflavour'=>'MARC21'
			);

			$sql = "INSERT IGNORE INTO biblio_metadata ";
			$sql .= "(biblionumber, metadata, timestamp, format, marcflavour) ";
			$sql .= "VALUES ('$row->biblionumber', ".$this->db->escape($row->marcxml).", '$row->timestamp', 'marcxml', 'MARC21');";
			$this->db->query($sql);

			if($this->db->affected_rows() > 0){
				echo " Success\n";
				$success = $success + 1;

			}else{
				echo " Failed\n";
				$fails = $fails + 1;

			}

		} //end foreach

		echo "=======END=============\n";
		echo "Total records : ".$q->num_rows()."\n";;
		echo "Success : ".$success." records\n";
		echo "Failed : ".$fails." records\n";

    } //end public function
}

View the issue in detail here http://koha.1045719.n5.nabble.com/Error-retrieving-biblio-in-rebuild-zebra-pl-line-680-td6010548.html