that shouldn't make a difference. you can have the same database on both sites. just make a new table and backup the old one and insert it into the new one. that way you can query the table on the new site. but if you must it is still possible as they are on the same domain.

when you connect to mysql you can choose more than one connection.

$conn = mysql_connect("localhost", $username, $password);
mysql_select_db($dbname, $conn);

that $conn can be any domain. localhost can also be an IP. if you were just doing 1 connection on 1 site it would be

$conn = mysql_connect("localhost", $username, $password);
mysql_select_db($dbname);

which would do the default one at the site.

but in each and every query you will have to specify the $conn along with the query.