I strongly suggest that you attend the official training to learn more about the controller functions...
http://www.extremenetworks.com/education/courses/ESE-HI-1/
Let's assume you run v10 as you didn't mentioned the installed software version.
On controller#2 in the GUI > AP > APs > Foreign > select all > Actions > Release
That should terminate the tunnel from controller#2 to the APs and the APs should open a tunnel to controller#1
Cheers,
Ron