To elaborate:
If you configured your AP System Profile to have a primary and backup LMS, then the APs would have failed over to the backup LMS upon loss of contact with their primary LMS. (Configuration > AP Group > AP > AP System > LMS Settings)
If you did not check the "LMS Preemption" box, they will stay on their backup controller until you reboot the APs. The Preemption box might be left unchecked to prevent the APs from having problems in the event of a flapping controller link, or repeatedly rebooting controller problem.
As for them failing to work after going to master, make sure you defined all the same VLANs on the Master as you had on your other controller. Anything beyond that will require more information from you on what exactly the APs are not doing after failing over to Master.