At my last sepm version i have not seen this problem after the upgrade i have seen a duplicate client entry in server. Search the client, one is online and other is offline.

Is this a version issue or some other problem?

Version is 12.1 RU4 MP1a

These clients are image system?

What is the last online date off that duplicate offline entry?

Check the article to repair it

How to repair duplicate IDs on cloned Symantec Endpoint Protection 12.1 clients

Article:TECH163349

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Created: 2011-06-27

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Updated: 2013-05-17

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Article URL http://www.symantec.com/docs/TECH163349

You can configure the setting to remove the old entry.

How to configure the number of days after which inactive clients will be deleted from the SEPM database.

Article:TECH93732

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Created: 2009-01-30

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Updated: 2010-08-18

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Article URL http://www.symantec.com/docs/TECH93732

See this articles

 In version 12.1 of the SEPM, the location for adjusting the setting to delete clients which have not connected for X number of days has moved:

1. In the SEPM, go to the Admin page.
2. Select Domains.
3. Under Tasks, select Edit Domain Properties.
4. In the Edit Domain Properties window, on the default General tab, note the option to "Delete clients that have not connected for specified time."

Duplicate SEP clients appear in the Symantec Endpoint Protection Manager console

https://www-secure.symantec.com/connect/articles/duplicate-sep-clients-appear-symantec-endpoint-protection-manager-console

Hi Hemant Singh,

 

I had similar problem, But when i try in my test enviorment before upgrading in production yes i has similar problem when I try to ugprade form SEP 12.1 Ru4 to SEP 12.1 RU4 mP1a. I check with symantec TECH support as there is not reported problem after I did repair on the client using the duplicate ID on clone, it worked fine.

But when I implement on the production I have not had that problem.

Please follow the article 

Title: How to repair duplicate IDs on cloned Symantec Endpoint Protection 12.1 clients
Article:TECH163349
Article URL http://www.symantec.com/docs/TECH163349

 

If you have same issue with multiple clients

Download client repair tool and rename as setup.exe and you can push to all the client.

Yea make sure you follow this procedure:

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

Can you post the screen shot? I have not seen such issues when we did the upgrade

Also let us know how did you confirm you have duplicate hardware I'd issue please update screenshot. It helps more to understand about your problem.