Yes. For example to update a quantity you could use something like:
function UpdateQuantityByID($cart,$id,$qty) {
for ($n=0; $n<sizeof($cart->Items); $n++) {
if ($cart->Items[$n]) {
if ($cart->Items[$n]->ID == $id) {
$cart->Items[$n]->Quantity = $qty;
$cart->SaveCart();
}
}
}
}