If you create a new Facebook App ID, then each user will have to approve the new application. Facebook also returns a different User ID for the same user across 2 different application IDs. Because of that, users that logged in on the old app won't be recognized by JFBConnect and each user would need to re-connect to their existing Joomla account.
If not, can Iuse Facebook Business to merge them?
The Facebook Business stuff allows you to look up users through a different API that we don't support. With that, you can check the User ID from App 1 and find the corresponding User ID for the same user in App 2. However, JFBConnect doesn't support that process as it's complex and there's no use case we've heard of to use it within a Joomla site.
Obviously, I'd really recommend to not create a new Application ID. Can I ask why you want to?
Thanks,
Alex