Just successfully updated the kernel, bootloader, device tree, and a whole bunch of other stuff following the advice in the response below. Simply hit “Reboot later” after all the updates installed, then copied the /boot on the NVMe to the /boot on the Jetson’s built-in eMMC, and then rebooted the Jetson. Obviously this is not the most ideal path and I’m still looking forward to us figuring out the boot issues so that the /boot folder (kernel, ramdisk, device tree, and so on) that’s actually booted from can live on the NVMe as well.