You can always remove the local controller's entry in the master. Then, upgrade the master and make sure that ALL config bits pertaining to the local are there. Verify that the RAPs came back as well. TAC is right..this should be an issue as the RAPs are already provisioned and once they re-communicate to the master post upgrade, they should also upgrade but be aware of Victor's boot partition note!!!!!
Now...once the master is upgraded, upgrade the local. Again, make your verifications there. Finally, add the local back into the master-local table and you are back whole.
I had a customer of mine do this method for 2 masters and 140 local controllers. Worked great!