Upgrading jetpack onto nvme without having to wipe out the system

Please refer to the following thread for the workaround about this issue.
JetPack 5.1.2/L4T 35.4.1 is now live - #9 by kayccc

Since there’s other partitions like bootloader, dtb…etc may be stored on the eMMC/SD. Just to verify if it would relate to your issue.

When you run apt dist-upgrade for debian based OTA update on your board(through serial console), there would be logs showed on your serial console. Please share them for further check.