.htaccess redirect blogs.dir to default WP uploads directory

I have a multisite that uses the Add Clone Sites for WPMU (batch) plugin to clone many thousands of sites at once. The plugin works great all except it is setting the media upload path to the old structure of the blogs.dir directory.

These are the three lines of code in the plugins files that I can find that is causing the problem:

update_blog_option ($new_blog_id, 'upload_path', 'wp-content/blogs.dir/' . $new_blog_id . '/files');

$dir_to_copy = ABSPATH . 'wp-content/blogs.dir/' . $template_id . '/files';

$dir_to_copy_into = ABSPATH .'wp-content/blogs.dir/' . $new_blog_id . '/files';

Should I change the above code to point to the default upload path or use an htaccess redirect? Either way, what is the default WP upload path?

Also, the reason I need this changed other than the obvious need for consistency across a large network, is because when I clone these sites the thumbnails from the template sites aren’t carrying through. The theme I’m using is called SportsMag by Magazine3 and they use timthumb (which I’m not a fan of), but because I finally got it working with the multisite thumbnail cloning, I need to fix this one plugin rather than change theme files again.

I appreciate all help and advice.