Whether it's ok to not choose "FLASH OS image to Target" During install-jetpak3.1.

install jetpak 3.1 in TX1 borad had installed jetpak3.0。
Whether it’s ok to not choose “FLASH OS image to Target” During install-jetpak3.1.
because, I had installed many many soft server in this TX1 board. if I must choose “FALSH OS image to Targe”, all soft server being installed is deleted.

Flash will delete all. You can clone an image though, and the image can be loopback mounted on your host (the image is the size of the entire file system…so probably about 16GB). The TK1 clone information is good, but the actual clone command differs. For information on cloning see:
http://elinux.org/Jetson/Cloning

EDIT: I have not yet cloned under R28.1, procedures may have changed. Basics under R27.1 and earlier (the URL below mentions a copy-and-paste edit to flash.sh which adds a “-G” option…I use this under R27.1 instead of the tegraflash.py commands):

# clone:
sudo ./tegraflash.py --bl cboot.bin --applet nvtboot_recovery.bin --chip 0x21 --cmd "read APP my_backup_image_APP.img"
# restore:
sudo ./tegraflash.py --bl cboot.bin --applet nvtboot_recovery.bin --chip 0x21 --cmd "write APP my_backup_image_APP.img"

(flash.sh script may make things a bit easier, under R27.1 there is )

For the actual clone command on a TX1, see:
https://devtalk.nvidia.com/default/topic/898999/jetson-tx1/tx1-r23-1-new-flash-structure-how-to-clone-/post/4784149/#4784149
http://elinux.org/Jetson/TX1_Cloning

You may be interested in copying part of your clone over to the sample rootfs. The boot directory is modified, so this part of sample rootfs should not be customized prior to a flash (most changes will be lost). However, I copy over my network configuration, ssh keys for the machine as a whole, and ssh keys of individual users into the sample rootfs. Software I’ve added is also copied over to sample rootfs. When I flash I immediately have a fully functional system with ssh key login, customized shell aliases, debug macros, so on. About all I need to do is set the GUI login autologout off and update packages. The trick will be to know what to copy…but if you have an entire loopback mountable clone of the original, then you essentially have access to your old Jetson even after it has been flashed and erased. Beware, cloning takes a lot of time, it’s about 16GB over a USB2 connection with slow eMMC.

As a side note, people who want an SD card for rescue, or find they must migrate to an SD card due to space restrictions may find a clone image a more interesting place to start for SD card content than the sample rootfs (you might still need to edit extlinux.conf and fstab). Imagine your SD card being an exact backup clone instead of a minimal system…you could literally copy the rescue byte-for-byte to the eMMC to restore that clone (you might still need to edit “/boot” content, but everything else is literally a clone).