When you update the Facebook App keys, any users that approved your old application will have to re-approve the new one. When they click the Login With Facebook button, the application permission dialog will show again, and, if they accept, JFBConnect will log them back in just like normal (they won't need to create a new account).
If that's not the behavior your seeing, let us know. There's no reason that changing the keys would 'break' integration, but it does add another approval dialog for your users on their first return after the update of the keys. Hope that helps explain what should be happening!
Problem of Kunena profile integration
