Sort the elements in the array. The first elements will be those without a value in the key, then those with a value.

arraySortingByKeyValue.php

<?php

$flatList = [
	[
		'id' => '3',
		'parentId' => '1',
		'parentSku' => ''
	],
	[
		'id' => '2',
		'parentId' => '1',
		'parentSku' => ''
	],
	[
		'id' => '1',
		'parentId' => '',
		'parentSku' => ''
	]
];

uasort($flatList, function($node) {
     return empty($node['parentId']) ? -1 : 1;
});

// Result is here http://joxi.ru/v29JwzZt47WkvA