In the config file for the second site, add;

PHP Code:
define('SITEMAPXML_SITEMAPINDEX''sitemap_store2');
define('SITEMAPXML_DIR_WS''sitemap_store2'); 
this will tell the module to create a new file, sitemap_store2.xml and use folder sitemap_store2 (create this manually through ftp).
Next create a new file in the root of your site called robots.php and add the next lines
PHP Code:
<?php
header
('Content-Type:text/plain');

echo 
'Sitemap: http://' $_SERVER['HTTP_HOST'] . '/' SITEMAPXML_SITEMAPINDEX '.xml' "\r\n";

echo 
'User-agent: *' "\r\n";
echo 
'Disallow: /cgi-bin/' "\r\n";
and may be other lines from your robots.txt file.

Next create if there is no .htacces file in your root or else edit.
search for RewriteEngine On . If it is not there add it.
after thet add : RewriteRule ^robots\.txt$ /robots.php [NC,L]

Next remove robots.txt from the root of the site. Now you have a dynamically created robots.txt that can adapt to any circumstance you want.