My upgrade went smooth but I accomplished mine using a tried and true process to keep me from destroying everything. Now this works fine if you have a simple installation of FreeNAS, but I will not guarantee it will work on a highly customized version where you have manipulated the crap out of it, you know like relocating where FreeNAS data is stored. It should work but nothing covers everything.
0) Backup anything you cannot afford to go away on your FreeNAS system.
1) If you are not running 9.2.1.6 or better, upgrade to it. I say this because I have read of people having some issue upgrading from 9.1.1 and honestly, why take the risk, but you can if you want. But if you are at 9.1.1 then you are not someone who lives on the technological edge so you could wait a few months for all the bugs to be ironed out.
2) Backup your config file and if you have encrypted drives, backup all that required data.
3) Shut down your system.
4) Remove your original USB Flash Boot Drive.
5) At this point you need to have downloaded the current stable FreeNAS .iso image and you will need to install it. There is more than one way to do this but I do not recommend using two USB flash drives to accomplish this, I do recommend the tried and true CD-R or you could use a Virtual Machine if you have one available, that works and you don't have to burn a CD-R.
6) If you have a CD drive in your machine, install the new Flash drive and FreeNAS CD, boot it up and install the software.
7) Follow the instructions and reboot your machine.
8) With any luck you will boot into FreeNAS.
9) Next reboot one more time for the hell of it and make sure it comes up.
10) Time to load your configuration file from the previous version and cross your fingers it works.
11) If it all fails and you toss your hands up in the air, turn off the machine and pop in your original USB flash drive, power on and wait for things to quiet down.
So what do you do if you have troubles?
If the problem was an invalid bootable drive, you may need to setup the proper device as the boot device in the BIOS.
If the problem was the CD-R didn't boot in your machine, you might have too old of a system, cross your fingers and check for a BIOS update.
If the problem was step 8 never booted into FreeNAS then check to ensure the flash drive is the boot device, the BIOS is updated.
Last ditch effort, if you have a free SATA port, install a SSD or hard drive to use as a boot device, ensure it is in the SATA0 port (first port) and is the boot device in the BIOS, install FreeNAS to it and cross your fingers it works.