John Vasta from the Jazz Foundation team explained clearly how to unregister manually applications.
My question here is how do we register them manually?
What are the exact steps for registering applications that are used in the JTS Setup process?
Please advise.
Thanks!

If you want to try and completely undo the CCM registration and redo, try these steps:

1. In the JTS admin UI, go to the "Registered Applications" page and remove the application
(click on the X at the right of the application entry). For CCM and QM, an error message will
appear at the top saying something like
"An error occurred while deleting the friend entry: b46a5e4af7f04cef81aaa1cd45799f98"; that can
be ignored.
2. In the JTS admin UI, go to the "Consumers (Inbound)" page and delete the authorized key
for the application (if there is one).
3. In the application's admin UI, go to the "Friends (Outbound)" page and remove the entry for
the Jazz Team Server (if there is one).
4. In the applications admin UI, go to the "Consumers (Inbound)" page and remove the authorized key
for the Jazz Team Server (if there is one).
5. Log out of the admin UIs and shut down the server that the application is running in.
6. Edit the teamserver.properties file for the application (e.g. server/conf/ccm/teamserver.properties)
and if there is a line containing the property name "com.ibm.team.repository.server.jts.url",
delete it.
7. Search for any files named "pending-jts-friend.rdf", and delete them.
For Tomcat, they will be somewhere under the server/tomcat/work/Catalina/localhost folder.
For WAS, they will be under the WebSphere/AppServer/profiles/<profileName> folder.
8. Restart the application's server.
9. Register the application. If the application is running in the same server as the JTS, you can just run
the JTS setup wizard again; it should detect that the application is available for registration.
If the application is running in a separate server, then it can be registered in the "Registered Applications"
page of the JTS admin UI. Then, the application's setup wizard must be run to finalize the setup.
_________________
John Vasta
Jazz Foundation Team