edd_change_uploads.php

<?php

function edd_change_downloads_upload_dir() {
    global $pagenow;

    if ( ! empty( $_POST['post_id'] ) && ( 'async-upload.php' == $pagenow || 'media-upload.php' == $pagenow ) ) {
        if ( 'download' == get_post_type( $_REQUEST['post_id'] ) ) {
            $wp_upload_dir = wp_upload_dir();
            $upload_path = $wp_upload_dir['basedir'] . '/edd' . $wp_upload_dir['subdir'];
            if (wp_mkdir_p($upload_path) && !file_exists($upload_path.'/.htaccess')) {
                if ($file_handle = @fopen( $upload_path . '/.htaccess', 'w' )) {
                    fwrite($file_handle, 'deny from all');
                    fclose($file_handle);
                }

            }
            add_filter( 'upload_dir', 'edd_set_upload_dir' );
        }
    }
}
add_action('admin_init', 'edd_change_downloads_upload_dir', 999);