Reading the document cjoseph linked, it looks like you would need to have extra licenses available for a seemless transition. It doesn't look like the identity of the APs is tracked by the centralized server, just the count. So they're not going back into the pool until 90 seconds later.
From my memory of going over license threshold, I believe the APs will switch to the new controller, but shut down their radios until those licenses free up at which point they'll begin working normally. Not an ideal answer, I know but if seemless failover is required, I guess you could still buy the extra licenses...