Programmatically Duplicate EntityQueues
I was able to get it to work, but I'm not entirely sure why it works. What I did was after saving the duplicated subqueue I loaded it once again then applied the items before saving for a second time. 

    $subqueue_clone-&gt;save();
    $newsubqueue_clone = \Drupal::entityTypeManager()-&gt;getStorage('entity_subqueue')-&gt;load($clone_id);
    $newsubqueue_clone-&gt;set('items', $clones);
    $newsubqueue_clone-&gt;save();