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Hi,
Yes, you have to re-flash the system. Please do
[1] Follow Quick Start section to download the system files for flashing Orin Nano developer kit. And follow the steps to Orin Nano developer kit.

Quick Start — NVIDIA Jetson Linux Developer Guide 1 documentation

[2] So now you have Linux_for_Tegra folder which is the default Jetpack release. And you can run initrd command to flash Orin Nano developer kit. Assume it is

~/jp61/Linux_for_Tegra

Please create a folder

~/jp61/src

Download source code to the folder and run

~/jp61/src$ sudo tar xpf public_sources.tbz2

And go to the directory for building kernel

~/jp61/src/Linux_for_Tegra/source

[3] You can follow the guidance to build kernel and NVIDIA oot modules

Kernel Customization — NVIDIA Jetson Linux Developer Guide 1 documentation

The path of installation is

$ export INSTALL_MOD_PATH=~/jp61/Linux_for_Tegra/rootfs/

After building/installing kernel and oot modules, please remember to do

$ cd ~/jp61/Linux_for_Tegra
$ sudo ./tools/l4t_update_initrd.sh

For Orin Nano developer kit, you shall not need to rebuild DTBs.

[4] Go to the folder and see if you can flash Orin Nano developer kit with self-built kernel image. Same initrd command should work

~/jp61/Linux_for_Tegra

[5] So now you can build and flash Orin Nano developer kit. And then you can enable/disable kernel cofigs for your use-case by modifying

arch/arm64/configs/defconfig
arch/arm64/configs/tegra_prod_defconfig

And re-do step [3][4]