To resolve this issue:
On the core,
1. To identify the Agent ID for the agent. Select the agent under Recovery Points Only data on the Core console.
The Agent ID will be found in the Web URL, for example, https://Core:8006/apprecovery/admin/ProtectedMachine/64e232ae-375d-40e3-8948-4860838d2336/Details. In this case the Agent ID is 64e232ae-375d-40e3-8948-4860838d2336. Copy this ID.
2. To identify the Agent ID for the new agent that is currently protected, and Agent ID is found in the Web URL but also in the registry of the Core. Open the registry and go to HKLM\AppRecovery\Core\Agents. You will see the Agents listed by Agent ID since it's a protected machine. Find the ID in question, select it, and the Display Name of the agent will be shown to verify against.
On the Agent.
3. Stop the Agent Service.
4. Open the registry and go to HKLM\AppRecovery\Agent\AgentId\. Export AgentId to desktop as back up. This is the ID of the new agent from step #2.
5. Double click DWORD for the Id registry key and replace the value with the correct Agent ID value that is from the original agent as copied from the core (from step #1).
6. Delete the AgentPairingSettings registry key (this key will be recreated after the agent is re-protected having the correct Agent Id - in step #9 below).
7. Start the Agent Service.
8. On the Core console, unprotect the agent by going to the agent > in the Summary tab > under the Actions drop down menu > Select Remove Machine (this is to remove existing protected agent having the incorrect agent id).
9. Protect the Agent and its recovery points will be paired together.
Windows Registry Disclaimer:
Quest does not provide support for problems that arise from improper modification of the registry. The Windows registry contains information critical to your computer and applications. Make sure you back up the registry before modifying it. For more information on the Windows Registry Editor and how to back up and restore it, refer to Microsoft Article ID 256986 “Description of the Microsoft Windows registry” at Microsoft Support.