I am not sure I understand fully, but maybe this will help?

   function showReplyBox(itemId,parentId)
   {
       var box = $('#comment-reply-box');
       var itemBox = $('#comment-item-'+itemId);
       var parent_id = $('#parent_id');

       parent_id.val(parentId ? parentId : itemId);

       $("#box").hide()

$('#replybox').remove().empty().append(box).append(itemBox).appendTo(
document.body)
   }

note: in your original code, you never re-added the #replybox to the DOM.

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