[Bug]: The append functionality works wrong in the 2.x branch

[slutsky]

Preconditions

The append functionality works wrong in the 2.x branch. When I try to add an additional fixture using $this->databaseTool->loadFixtures($fixtures, true) I loose all previous references.

Steps to reproduce

In ConfigMysqlTest::testAppendFixtures() I added an additional check:

public function testAppendFixtures(): void
{
    $this->databaseTool->loadFixtures([
        'Liip\Acme\Tests\App\DataFixtures\ORM\LoadUserData',
    ]);

    $referenceRepository = $this->databaseTool->loadFixtures(
        ['Liip\Acme\Tests\App\DataFixtures\ORM\LoadSecondUserData'],
        true
    )->getReferenceRepository();

    // Expected 2, but 1 returned.
    $this->assertCount(2, $referenceRepository->getReferences());

Expected result

All tests with additional check pass.

Actual result

Tests are broken.