<?php 

$o1 = new stdClass;
$a = 'd';
//This is the base array or the initial structure
$o1->ar1 = ['a', 'b', ['ca', 'cb']];
$o1->ar1[3] = & $a; //set 3rd offset to reference $a

//direct copy (not passed by reference)
$o1->ar2 = $o1->ar1; //alternatively array_replace($o1->ar1, []);
$o1->ar1[0] = 'z'; //set offset 0 of ar1 = z do not change ar2
$o1->ar1[3] = 'e'; //$a = e (changes value of 3rd offset to e in ar1 and ar2)

//copy and remove reference to 3rd offset of ar1 and change 2nd offset to a new array
$o1->ar3 = array_replace($o1->ar1, [2 => ['aa'], 3 => 'd']);

//maintain original array of the 2nd offset in ar1 and change the value at offset 0
//also remove reference of the 2nd offset
//note: offset 3 and 2 are transposed
$o1->ar4 = array_replace_recursive($o1->ar1, [3 => 'f', 2 => ['bb']]);

var_dump($o1);