array([0]=> 'email@email.com', [1]=> 'email2@email.com', [2]=> 'email3@email.com');

$emails = join(', ', $emails);
    $sql = "DELETE FROM emails WHERE customer_id='".$id."' AND email NOT IN(".$emails.")";
    $query = $this->db->query($sql);

$sql = "DELETE FROM emails WHERE customer_id='".$id."' AND
        email NOT IN('".implode("','",$emails)."')";

$emails = implode("', '", $emails);
$sql = "DELETE FROM emails WHERE customer_id='".$id."' AND email NOT IN('".$emails."')";
$query = $this->db->query($sql);

$emails = implode("', '", $emails);
$sql = "DELETE FROM emails WHERE customer_id='".$id."' AND email NOT IN('".$emails."')";
$query = $this->db->query($sql);

$emails = join('", "', $emails);
$sql = 'DELETE FROM emails WHERE customer_id="'.$id.'" AND email NOT IN("'.$emails.'")';
$query = $this->db->query($sql);

$emails = join(',', $emails);
To avoid comma in last ,
$emails=trim($emails,',');
$sql = "DELETE FROM emails WHERE customer_id='".$id."' AND email NOT IN(".$emails.")";
$res = $this->db->query($sql);