If you have an environment where you have upgraded to CU5 but you have manually installed agents the process to upgrade to CU5 is intensive. If your manually installed agents are NOT as a result of network communication restrictions, this approach is one that has been used to use the OpsMgr console to perform the CU5 upgrades by a client I have been working with. This is not a supported or recommended approach in most situations but is being provided to discuss the steps involved.

1) Using the queries specified in the Kevin Holman article at http://blogs.technet.com/b/kevinholman/archive/2010/02/20/how-to-get-your-agents-back-to-remotely-manageable-in-opsmgr-2007-r2.aspx, update all desired Servers to be Remotely Manageable that are not network restricted. Again, do not do this for clients which cannot have agents pushed to them – it will not work and will only make things worse.

SQL Query:
UPDATE MT_HealthService
SET IsManuallyInstalled=0
WHERE IsManuallyInstalled=1

2) From Administration in the OpsMgr console, under Agent Managed, once the view updates to reflect the agents as Remotely Manageable = Yes, you can right click on the agent and Select Repair.

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3) Under the Pending Management tab you can track the repair Operation to verify it succeeded.  If it does not, you will see that as well. If it Fails, you can simply REJECT the agent listed under Pending Management= Repair Failed.  This will NOT remove the agent from the Agent Managed List.  You will need to verify why the operation failed.  Usually this is caused by a firewall causing an RPC connection failure pushing the update package, but you will have to investigate for your environment to determine the cause.

4) Once the repair completes, you can expedite the rediscovery of the updated agent by flushing it’s health service state.  This can be done a couple of different ways:

a. From the Discovered Inventory pane in the Monitoring area by selecting  “Agent” as Target type, select the agent you wish to flush, use the actions pane on the right of the screen and select “Flush Agent Health State and Cache” 

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b. You can log into the box, stop the agent, delete Health Service State Folder (or rename it), then restart the agent.

5) Give it time to rediscover and post the data.  Once it has completed, you will see the latest CU listed when you check the properties for the agent from the Discovered Inventory pane (with Agent selected as Target Type).
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Thank you to Louis Oliver for putting this together!