yes, that’s APP partition to contain all your user data, please back-up system.img for your use-case;
you should restore the image with the same release version.
for example, if you back-up system.img from JP-4.6, you should restore the image to JP-4.6 flashed targets.
you should use the command-line to do this. you could use the same JetPack release you’ve download, please enter the installation folder,
the default path is… ~/nvidia/nvidia_sdk/JetPack_<version>_Linux_<platform>/Linux_for_Tegra/
there should be script file, flash.sh available, please follow the commands to backup/restore your image.