This test fails:

<?php

public function testReplaceWithLongerPathKeepsOrder()
{
    $path = new PropertyPath('new1.new2.new3');
    $expected = new PropertyPath('new1.new2.new3.old2');

    $builder = new PropertyPathBuilder(new PropertyPath('old1.old2'));
    $builder->replace(0, 1, $path);

    $this->assertEquals($expected, $builder->getPropertyPath());
}

generating new1.new2.old2.new3 instead of new1.new2.new3.old2.

PropertyPathBuilder::replace modifies the elements array correctly, but does not re-sort the array.
A foreach is then executed against $this->elements to create the PropertyPath object, resulting in a wrong path to be generated.

A simple ksort at the end of the replace method should be sufficient.