I had missed this thread until I noticed your Bug#370 being solved.
Just to confirm your question / answer. Yes, power off the chip (front panel rocker switch - or telnet into SCC and issue power off) Then power off the board via the switch on the power supply located at the back of the SCC. As an extra precaution, I also remove the power cord to the SCC power supply.
As noted, it is important to run autotrim before powering on the chip for the first time.
Good to hear you have your system back up and running.