Paw,
You can set a DHCP option on the MPLS subnets that the APS are on to point to the local controller. http://www.arubanetworks.com/techdocs/ArubaOS_64x_WebHelp/Web_Help_Index.htm#ArubaFrameStyles/DHCP_Option_43/Windows_Based_DHCP_Serve.htm?Highlight=dhcp option 60. If your APs are located in a subnet shared by your local controllers, it will first locate the local controller via broadcast, as well.
What either one of those things wil will do, is make the AP always discover the local controller first when it reboots. That is because finding a controller via a local broadcast at boot and finding a controller with a DHCP 60/45 option at boot, overrides DNS discovery (which might point to your master controller).
In addition, if you have a backup LMS-IP in the AP group for your MPLS APs that points to the master controller, you should remove it, so that the APS do not fail over to the master during your upgrade; temporarily.
The end result, is that your APs will always find the local controller when it boots and when it upgrades. When the upgrade is over, you can put the backup LMS-IP that points to your master controller back in, if it was there in the first place.
In summary:
Puting a DHCP Option 45 and 60 that points to the local controller on the MPLS subnet(s) that have your APS or having your APs in the same VLAN as a controller will override DNS discovery of the master controller. In fact, it is a best practice so that APs always find the local resource first, rather than the master controller, over the WAN..