Rowid : The row ID is a unique identifier that is generated by the cart code when an item is added to the cart. The reason a unique ID is created is so that identical products with different options can be managed by the cart.
Every item in cart has a rowid element and by rowid you can update cart item.
$updateItem = array( 'rowid' => 'b99ccdf16028f015540f341130b6d8ec', 'qty' => 3 );
and then below code