I'm really confused. The .qxp shouldn't show hierarchy. If you make assignments to nodes in the hierarchy it will, but that's because it has to(the only way to point to a lower level file is through hierarchy). That being said, the hierarchy is in your design, not the .qsf. Maybe if you can explain what someone else is doing with your project without the RTL, or something like that, it would help. Right now my assumption is that you want to give someone a project(which has hierarchy in the HDL, independent of the project), but don't want them to know the hierarchy?