Cloning the image
To make a carbon copy of an existing Jetson install, first connect the Jetson's micro-B USB flash port to the Linux machine that you originally flashed L4T from. Then enter the Jetson into recovery mode by holding RECOVERY and pressing RESET.
cd into the Linux_for_Tegra/bootloader directory that you used when originally flashing the Jetson. Inspect flash.cfg to obtain the partition id of system.img (in this case, 9)
[partition] name=APP id=9 type=data allocation_policy=sequential filesystem_type=basic size=15288238080 file_system_attribute=0 partition_attribute=0 allocation_attribute=8 percent_reserved=0 filename=system.img
Next, remove the old system.img built from the initial flashing and download the new image from the Jetson. If the id of your system.img partition is different than 9, substitute that in the nvflash command.
sudo rm system.img sudo ./nvflash --read 9 system.img --bl fastboot.bin --go
(downloading the image can take a while)
The image can be restored to a Jetson by flashing it with the -r 'skip building and reuse existing system.img' flag:
cd ../ sudo ./flash.sh -r -S 14580MiB jetson-tk1 mmcblk0p1
Reboot the Jetson when it's done flashing and the system should be restored to the state at the time of cloning.
Keep the Linux_for_Tegra directory used during the cloning process to successfully restore the image. Linux_for_Tegra/rootfs can be removed as it's no longer needed. However the other L4T files should be transported along with the system.img to use during restoration.
sudo rm -r -f rootfs cd ../ tar -zcvf my_backup.tar.gz Linux_for_Tegra
tar.gz can significantly compress the size of system.img and will retain the access privileges and is now convenient to copy/FTP/ect.