That's why they decode it with qpdf and re-encode it again afterwards, so qpdf takes care of that. qpdf reconstructs the original PDF structure, and I think it

That's why they decode it with qpdf and re-encode it again afterwards, so qpdf takes care of that. qpdf reconstructs the original PDF structure, and I think it even tries to keep the object numbers the same, but the offsets are recalculated completely.