The “kernel-4.9/” is where you compile the kernel from. In some cases there are references to kernel code not in the main kernel, and this will use a relative path naming code in the other subdirectory. Also, there is sometimes bootloader code in other subdirectories, and this can be compiled from that location…but this too might use a relative path to reference code in the kernel. Don’t erase any of it.
You might find this of interest:
- https://forums.developer.nvidia.com/t/how-to-fix-xorg-conf-in-jetson-orin/229155/12
- https://forums.developer.nvidia.com/t/problem-smb-jetson-nano/193640/11
Before you start be sure to examine the output of the command “uname -r”. Then you copy the existing configuration (and if this is stock, then that is just the “make tegra_defconfig” command), and then make edits (such as via “make menuconfig”, although I prefer “make nconfig” since it has a symbol search function).