Upgrading PixHawk firmware from 3.1.2 to 3.3-rc5

I currently have an Iris quadcopter which has a PixHawk with 3.1.2 firmware installed.

I'm getting a "Failure : unsupported command 400" when trying to "arm throttle" through APM Planner on Windows and pymavlink on Linux (however it can be armed with the RC controller no problem as expected).  Can anyone confirm or deny that this is an incompatible MAVlink/firmware problem?

The latest firmware for Arducopter is 3.3-rc5.  Does anybody have experience upgrading to this version?  Does anybody know if the PID / configuration will be reset (as in we don't have to recalibrate everything manually)?  I've used the APM planner to download the current config file so I can re-inject once the firmware is updated just in case.

Thanks.

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