Umair,
First off, JFBConnect v4.0 is quite old. We'd highly recommend having your brother upgrade. The newest release is v4.2, and has a lot of improvements and bug-fixes over the release you are apparently using.
Regarding your other questions:
1) Switching a template won't remove your comments as long as the URL stays the same. The comments are tied to a specific URL. There's no way to import or export comments, they are all stored on Facebook.
2) Yes, you can delete or mark comments as spam.
3) Yes, you can have multiple moderators (even for specific sections of your site) who have the ability to moderate comments.
If you need help setting up #2 or #3, we can gladly help. However, please have your brother post this this thread using his account with an active subscription. Priority support for help setting up things like moderation for comments is for active subscribers only, and is included with the subscription.
Thanks,
Alex