Just after a bit of clarity around this, from the 6.3.1.16 release notes:
In a Master / Local deployment, all controllers need to be running the same ArubaOS version. Controllers ina Master / Local deployment do not support different ArubaOS.
I think the "correct" upgrade method is to load the software on both, then reboot them at the same time.. however, what I would like to do is move all the APs onto the local controller (we terminate across both master and locals and control distribution by lms), upgrade the master, reboot, move the APs back, so they upgrade, then do the local, reboot, the distribute the APs back.
Would I be ok doing this?
This way would have less impact on the site as a whole, as I could move small groups between the controllers, which may take a little longer, but give me more control...