Sorry for reviving this old thread. I just wanted to let people to know that I successfully did this on FreeNAS11.1-U4 with a RAIDZ1.
Also note that there is a new Resilver Priority (Storage) feature in the GUI that might help speeding up the process a little.
With re-keying, re-passphrasing and adding a new recovery key before rebooting I managed to retain all my jail, sharing, snapshot etc. configurations.
I am trying this method on my mirror setup FreeNAS11.1-U5 with a RAIDZ2. Successfully went through steps 1-7, so all single disks are encrypted. If I understand the latest posts on this thread, some users managed to re-key, re-passphrase before reboot, avoiding the lose of Jails and other config.
I would be interested to know how the re-keying, re-passphrasing and adding new recovery key before reboot works. In the GUI, the buttons related to encryption are not present. On the CLI, not sure which command is the right one to re-key. Maybe:
You must go through the whole process up until step 13 for the encryption related buttons to appear in the GUI. Then you can re-key etc. in the GUI (for the GUI and management system to remember that your disks are now encrypted).
It is important that you re-key and re-passphrase before you reboot (but after finishing the rest of the steps) to save your jails and configuration.