Where do you boot NL from ? If from a USB key, prepare and install NL on another key, plug-in the server and boot. You'll see fast enough

But, don't worry, your data will not have any problems if it doesn't boot correctly (I don't know if the config file has changed between the versions).
Same procedure if you boot from a CF card.
If you boot from a hard drive, I'd unplug all the data drives before doing the re-install.
Worst case scenario, you have to set all the parameters back again.
What didn't go well with the new version ?
Robby