gistfile1.txt

type "mysql" when logged in as root via SSH and then paste this:

UPDATE `database`.`files` SET filepath = REPLACE(filepath, 'sites/olddomain.com/', 'sites/newdomain.com/');
UPDATE `database`.`node_revisions` SET body = REPLACE(body, 'sites/olddomain.com/', 'sites/newdomain.com/');
UPDATE `database`.`boxes` SET body = REPLACE(body, 'sites/olddomain.com/', 'sites/newdomain.com/');

NOTE: "database" should be replaced with your site's database name from settings.php created by Aegir.
      "olddomain.com" and "newdomain.com" should be replaced with existing and expected (sub)domain.