Objects have to be passed by reference explicitly if function is replacing original object with cloned one.

reference.php

<?php

class A {
    public $property = "Default Value";
}

function clone_and_modify(A $obj) {
    $cloned = clone $obj;
    $cloned->property = "Modified Value";

    return $cloned;
}

function pass_by_explicit_reference(A &$obj) {
    $obj = clone_and_modify($obj);
}

function pass_by_implicit_reference(A $obj) {
    $obj = clone_and_modify($obj);
}


$obj1 = new A();

pass_by_explicit_reference($obj1);
var_dump($obj1->property);

$obj2 = new A();

pass_by_implicit_reference($obj2);
var_dump($obj2->property);