gistfile1.php

<?php
/**
 * Plugin Name: Update Previous Order Numbers for EDD
 * Description: For users of the sequential order number beta, use this before you get new orders to have your previous orders sequentially numbered
 * Version: 0.1
 * Author: Chris Christoff
 * Author URI: http://www.chriscct7.com
 */

function update_script_edd_seq_numbers(){

	if( ! isset( $_GET['edd_order_upgrade'] ) ) {
		return;
	}

	$args = array (
		'post_type' => 'edd_payment', // we only want orders
		'posts_per_page'=> -1, // get all the orders at once
		'order' => 'ID', // same as below 
		'orderby' => 'ASC', // we want to order the smallest order as order #1
		'fields' => 'ids', // we just need the ids
	);
	
	$orders = new WP_Query( $args ); // we hath the orders
	
	$current_order_number = 1; // first order is #1
	$prefix = ''; // stuff before the number
	$postfix = ''; // stuff after the number
	
	foreach($orders as $order){ // let's renumber all orders 
		$order_number = $prefix.$current_order_number.$postfix; // here's the new order number
		update_post_meta($order,'_edd_payment_number', $order_number); // let's update that order
		$current_order_number++; // increment the order number
	}
}
add_action( 'admin_init', 'update_script_edd_seq_numbers' );