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I think this depends a bit on what you want. The 'firmware' actually consists of separate layers: u-boot, kernel and rootfs. These are all files on partitions, so as long as the edison has booted you can update these by copying the files you need to update, via f.i. wifi and ssh.
Or if you have packages (.deb, .ipk, .rpm) you can update by copying the package and running the appropriate installer (dpkg -i *.deb).
If the Edison will not boot, or you want to flash a complete image, and u-boot still works, you can flash using dfu (via the usb port). This can be done with the flashall script.
If you broke u-boot itself, you need xfstk (which is called from flashall --recovery). This requires acces to the usb port as well.
If you don't need to update the kernel or u-boot, you can have the rootfs on a sd card. And then update by placing a new sd card.
You might find some useful details here: Build and flash U Boot separately · htot/meta-intel-edison Wiki · GitHub
It is probably possible to flash using jtag, and it would be nice to know how. Anybody?
Thanks for the reply, very helpful.