Hello,
in HyperMesh 13, you can mark unused free nodes or temp nodes as 'preserved nodes', if you want to keep them in your model. This guarantees, that the free nodes still be available after saving a HyperMesh file. Please see the attached video on how to convert a free node to a preserved node:
http://screencast.com/t/anpycRBs
You can also consult the online help for the 'preserved nodes' panel for further information.
Jan