Just reporting back on this.
I downloaded the FreeNAS 9.10.1 ISO from the website, and mounted it from IPMI.
Booted from the device, and went into shell, and did a
> ZPool import
(...import, because I thought I was done for...)
It commented that everything was in use by another system,
so I did a
> ZPool import | less
and noted the gptid's of my freenas-boot pool (mirrored usb's in my case)
Then I got the device ids by doing a
> glabel list | grep -B 2 -A 10 <gptid-1>
> glabel list | grep -B 2 -A 10 <gptid-2>
This listed the device id's as da12 and da13.
I then exit'ed the shell,
choose install/upgrade,
selected da12+da13,
and the installer asked if I wanted to upgrade or re-install.
I choose upgrade, waited, rebooted,
the freenas boot menu presented it self.
During boot, I now get a blank (black) screen,
but I noted that my DHCP (BOOTP) said the freenas IP was online.
So I entered the ip into a browser, and got "FreeNAS-9.10.1 (d989edd)" uptime 2 min.
Jails and plugins are running, and apart from the blank shell in IPMI, everything seams good.
EDIT:
As a side note, it would be awesome, if the installer could indicate which devices contain a freenas install already.
But seeing as I hope not to be doing this again for some time, it is a minor issue. ( GUI upgrade not borking grub would be better :) )