Split invoice in Magento into two invoices, one for virtual and one for non-virtual products

splitMagentoOrderIntoTwoInvoices.php

<?php

chdir(dirname(__FILE__));

require_once '../app/Mage.php';
Mage::app();
umask(0);

$resource = Mage::getModel('core/resource');
$db = $resource->getConnection('core_write');

$order = Mage::getModel('sales/order')->load(1);
$sendEmail = true;
                    
$productModel = Mage::getModel('catalog/product');

$virtuals = $nonVirtuals = 0;

foreach($order->getAllItems() as $orderItem) {
    if($orderItem->getQtyInvoiced()==$orderItem->getQtyOrdered()) continue; // skip already invoiced items
    $item = Mage::getModel('sales/convert_order')->itemToInvoiceItem($orderItem);
    $_product = $productModel->load($item->getProductId());
    if($_product->getTypeId() == Mage_Downloadable_Model_Product_Type::TYPE_DOWNLOADABLE) {
        // Virtual
        $virtuals++;
        $virtualQtys[$item->getOrderItemId()] = $orderItem->getQtyOrdered();
        $nonVirtualQtys[$item->getOrderItemId()] = 0;
    } else {
        // Non-virtual
        $nonVirtuals++;
        $nonVirtualQtys[$item->getOrderItemId()] = $orderItem->getQtyOrdered();
        $virtualQtys[$item->getOrderItemId()] = 0;
    }
}

/* Save non-virtual invoice first; it will contain shipping costs */
try {
    $nonVirtualInvoice = Mage::getModel('sales/service_order', $order)->prepareInvoice($nonVirtualQtys);
    $nonVirtualInvoice->register(); // be sure to use register() instead of save(); otherwise the 0 qty items will be displayed as well and the individual order lines will not be set to 'invoiced'
    $nonVirtualInvoice->setEmailSent($sendEmail);
    $nonVirtualInvoice->getOrder()->setCustomerNoteNotify($sendEmail);

    $transactionSave = Mage::getModel('core/resource_transaction')
        ->addObject($nonVirtualInvoice)
        ->addObject($nonVirtualInvoice->getOrder())
        ->save();
} catch(Exception $e) {
    die($e->getMessage());
}

/* If it has been split, save the virtual invoice as well */
if($virtuals > 0 && $nonVirtuals > 0) {
    try {
        $virtualInvoice = Mage::getModel('sales/service_order', $order)->prepareInvoice($virtualQtys);
        $virtualInvoice->register(); // be sure to use register() instead of save(); otherwise the 0 qty items will be displayed as well and the individual order lines will not be set to 'invoiced'
        $virtualInvoice->setEmailSent($sendEmail);
        $virtualInvoice->getOrder()->setCustomerNoteNotify($sendEmail);
        
        $transactionSave = Mage::getModel('core/resource_transaction')
            ->addObject($virtualInvoice)
            ->addObject($virtualInvoice->getOrder())
            ->save();
    } catch(Exception $e) {
        die($e->getMessage());
    }
}

if($virtuals > 0 && $nonVirtuals > 0) {
    echo('Order ' . $order->getIncrementId() . ' has been split into ' . $nonVirtualInvoice->getIncrementId() . ' and ' . $virtualInvoice->getIncrementId());
} elseif($nonVirtuals>0 && $virtuals == 0) {
    echo('Order ' . $order->getIncrementId() . ' has been transformed into one non-virtual invoice; ' . $invoice->getIncrementId());
} elseif($virtuals > 0 && $nonVirtuals == 0) {
    echo('Order ' . $order->getIncrementId() . ' tried to be invoiced but has virtuals but no non-virtuals; this should be handled elsewhere');
} else {
    echo('Order ' . $order->getIncrementId() . ' has no items to invoice');
}
echo "\n";

It works fine. I have rewrite invoiceController it is working for me but having issue of subtotal in separate invoice.Separate invoice display total of it's order.