While I wrote this back, I got an answer from Canaan support who have been helping but think they are leading me the wrong way with this particular unit. They told me this 1166Pro-68 cannot run with 2 boards as it's not designed to, so deliberately disconnecting it causes this issue (but ignored that it has worked once previously and never again) - they supplied some software and told me to use 'Power Mode 4' so I can run it at 64% but FMS can set it which makes me think it's for 12 and 13 series miners.
I reattached the middle board (H2) and the miner works fine and normally, no issues (log attached bottom of message) - so I don't think there is a comms error on the other two boards:
If that's what they said then you can't run this unit with only two hashboard. I don't know about power mode 4 using the FMS app you can only find two options there under switch mode "normal mode and high performance mode" There is no power mode 4 on the FMS app you can maybe try to send a command to adjust the power to these two hashboard check the command below and send this command using FMS app under diagnose and don't forget to replace 1260 below and test if it would work with only 2 hashboard.
[{"command":"ascset", "parameter":"0,hashpower,1260"}]