$sql = "SHOW TABLES FROM database";
$tablas = Db::getInstance()->executeS($sql);

foreach ($tablas as $tabla) {

    //Consultamos si la tabla contiene el campo id_shop
    $result = Db::getInstance()->executeS("SHOW COLUMNS FROM `".$tabla['Tables_in_database']."` LIKE 'id_shop'");

    if ($result) {

        //La tabla tiene el campo id_shop

        //cambiamos la ID de la tienda principal a 3
        $sql = "UPDATE ".$tabla['Tables_in_database']." SET id_shop = 3 WHERE id_shop = 1";
        Db::getInstance()->execute($sql);

        //Cambiamos la ID de la tienda secundaria a 1
        $sql = "UPDATE ".$tabla['Tables_in_database']." SET id_shop = 1 WHERE id_shop = 2";
        Db::getInstance()->execute($sql);
    }
}