After some USB related issues I managed to flash my Orin NX using this config: Jetson Orin NX + Xavier NX Devkit (NVMe)
and this guide:
https://docs.nvidia.com/jetson/archives/r35.2.1/DeveloperGuide/text/IN/QuickStart.html#to-flash-the-jetson-developer-kit-operating-software
The culprit ended up being tlp on my host ubuntu - most likely something to do with the USB suspend involved…