The controller will change the config so it is suitable for the new code (allowing syntax changes, new commands, etc...) When you controller has rebooted, it will still do what it used to, it won't lose WLAN configs, IP addressing, etc...
When upgrading code, also remember that the APs will need to download their new code too, which takes about 3mins, and the controller can upgrade 10APs at a time. Therefore;
Total outage = Controller Outage + AP Outage
So if you have a hundred APs, the total time before the last AP returns to service is..