No, you don't have to configure it manually. Just do the following to have JFBConnect automatically configure the app again for you:
* Create a new app in the Facebook Developer area
* Get the Facebook App ID and Secret Key
* Enter Autotune in JFBConnect and go to the "Basic Info" menu item on the left
* Replace the old App ID and Secret Key and hit "Save"
* On the FB App page, hit the "Refresh" button. That will then detect that your settings have changed and recommend new ones.
* Simply hit "Use Recommended Settings" at the bottom
That should re-configure your app with all of the recommendations JFBConnect would have originally set it up with. You can change any values from there to suit your needs, if necessary.
Once that's done, you should be set. If you had previous users registering on your site, they will need to re-approve the new application. However, once approved in the login popup, they will still be logged into the same Joomla account. So, other than that little hiccup, your users shouldn't see any difference.
Hope that helps, and good luck!
Alex