Hi spanner,
It is common for a user to change the OS on a PXI controller. I suggest you take a look at the tutorial Restoring or Changing the Operating System in a PXI-8171 Series Embedded Controller at http://zone.ni.com/devzone/conceptd.nsf/webmain/26F082D561C912BB86256D080074AD58?opendocument.
When you run winnt, it should copy the necessary installation files. You will then need to reboot your computer. When prompted, you will need to select the option to setup Windows.
Regards,
David Shatila
Applications Engineer
National Instruments
www.ni.com/support
1-866-ASK-MY-NI