You have not mentioned which version you are using, but you will have a directory “~/nvidia/nvidia_sdk/”, and within that a “JetPack_…” with a version such as “4.2” or “4.2.1”, followed by “_Linux_P3310”. As an example I am going to use “~/nvidia/nvidia_sdk/JetPack4.2_Linux_P3310/Linux_for_Tegra/”, but adjust for your release case. This is the driver package. The “rootfs/” subdirectory is the sample rootfs package (plus apply_binaries.sh added to it).
If running this has resulted in downloading the flash software you will have some files in the driver package directory. You will also have an entire set of operating system files in the “rootfs/” subdirectory. If those are there (and they would be if you’ve reached the stage where flash could start), then you will be set with a simple command line. If not, then something got in the way of setup.
If you do have those files, then with the TX2 in recovery mode you can flash via this from the driver package directory:
sudo ./flash.sh jetson-tx2 mmcblk0p1
If recovery mode is correct, then you should see some output from:
lsusb -d -0955:7c18
I’m not sure what would go wrong where it doesn’t offer to flash from the GUI, but maybe there isn’t enough disk space. See if you have space of type ext4 at the driver directory:
df -H -T ~/nvidia/nvidia_sdk/JetPack4.2_Linux_P3310/Linux_for_Tegra/
If you use a VM on the host then there are a number of expected USB issues.