The question of Linux filesystem is basically determining whether permissions were preserved. A host being Linux does not necessarily mean this is a Linux file system type (for example a live DVD won’t work…it isn’t a native Linux file system type…and some VMs try to install on NTFS…this too won’t work even though Linux runs on it).
You can use “df -H -T .” from the location of the flash.sh script and you’ll know for sure…it should be ext4.
A second place this might fail is if you used command line flash and did not use sudo with the apply_binaries.sh step.
If you used command line flash and did not unpack the sample rootfs with sudo this would also cause permission failure.
In the cases above “sudo” from the Jetson will tend to fail. Not being able to access the “.ssh” directory is very suspicious of permissions, sudo, and/or how the root file system was created being in error.
You might also try a simple “sudo ls” and see if it works.