it downloads the config, loads it and reboots to the new config connected to the controller.
EDIT: It's been a while since I've used it, but your phone will connect to the AP's "island" wifi and push the config from your phone to the AP which will then reboot and attempt to connect to the controller. The initial steps of scanning the AP thru swipe only adds that AP's information to the controller, lets you assign a name, zone, etc. but that does NOTHING to the AP itself. Bootstrapping connects to the AP (assuming it's powered on) and pushes the config to it.