There is a scenario where 2 systems are havin same Unique ID, Hardware Key and UUID. When one system is showing in Group other is not showing and vice versa. Both the system have different ip and host name.

How to show both the system in the group.

You need to clear out the duplicate IDs

TECH163349   Repair duplicate IDs on cloned Endpoint Protection 12.1 clients

How to prepare a Symantec Endpoint Protection 12.1.x client for cloning

You need to clear the Hardware IDs on both the machines so that they generate new IDs and get registered as two different machines.

You almost got your answer in your question. Clear the HWID in both the PC's. That will fix the issue.

1.  Stop SMC on both of the affected client computers by clicking Start> Run, type smc -stop then click OK. 
2.  On the SEPM console, delete the client entry that the two computers have been sharing. This will prevent the client duplication that would otherwise occur due to the following steps. 
3.  On each of the affected computers, go to registry location:  
     HKLM\Software\Symantec\Symantec Endpoint Protection\SMC\Sylink\Sylink 
4.  Clear the value for "Hardware ID." (make it blank) 
5.  Disable Tamper Protection if you are unable to edit the value. 
6.  On each of the affected computers, navigate to the following directory location: 
     SEP 11 Location:   
        C:\Program Files\Common Files\Symantec Shared\HWID 
     SEP 12.1 Location:  
        Windows XP/2003: C:\Documents and Settings\All Users\Application Data\Symantec\Persisted Data 
        Windows Vista/7/2008: C:\Program Data\Symantec\Symantec Endpoint Protection\Persisted Data 
7.  Find file "sephwid.xml". Rename it to "sephwid.xml.bak". 
8.  Start SMC on each computer by clicking Start> Run, type smc -start then click OK. 
9.  Check the SEPM console for the new SEP client  
     When the clients check in they should have unique hardware IDs.

Follow the symantec article to remove the dupli cate hardware id for the visibility of both clients

Duplicate Hardware IDs result in only one client showing up in the Symantec Endpoint Protection Manager for multiple systems