Folowing example is selfexplaining the issue:

$r = Doctrine_Manager::getInstance()->getQueryRegistry();

// Add new query - list ordered by permission attribute
$q1 = Doctrine_Query::create()->from('sfGuardUser')->orderBy('username');
$r->add('sfGuardUser/list', $q1);
var_dump($q1->getDql()); // string(35) " FROM sfGuardUser ORDER BY username"

// Get this query from registry and adjust it
$q2 = $r->get('list', 'sfGuardUser');
$q2->orderBy('password');
var_dump($q2->getDql()); // string(35) " FROM sfGuardUser ORDER BY password"

// Try to get original added query from registry
$q3 = $r->get('list', 'sfGuardUser');
var_dump($q3->getDql()); // string(35) " FROM sfGuardUser ORDER BY password" 

If you add query to registry, get it again and adjust via fluent query interface, you change query object in registry. That is not expected behavior, i think.. IMHO the solution is cloning query before adding and before returning.