I was deploying System Center Operations Manager 2007 R2 on clustered RMS for a client when we had a failure/corruption of the Windows cluster. After creating a new Windows cluster and reinstalling my RMS cluster I had an other issue. Agents already install were showing up in the console but the status was Not Monitored even after several hours. I tried to do a repair and also tried to do a Modify on some servers but nothing. After seeking on Internet I found a solution but it was for removing the agent on one server using command line. Unfortunatly I needed to remove over 250 agents! I noticed other were also looking for a way to remove agents on several servers so here it is.

The easiest way to remove SCOM agent from a machine is to use one of the following command line (if you are not sure which version you got, follow the procedure here):

Uninstall R2 Agent
msiexec /x {25097770-2B1F-49F6-AB9D-1C708B96262A} /qn /norestart
Uninstall SP1 Agent (slipstream only, not RTM upgrade)
msiexec /x {E7600A9C-6782-4221-984E-AB89C780DC2D} /qn /norestart

Uninstall SP1 Agent (RTM > SP1 upgrade)
msiexec /x {768DB8BD-CB3A-43F4-9A4C-BA2921D27AD3} /qn /norestart

Now if you have to remove the SCOM agent from several servers, you can use PSexec to do it. You will need the list of servers on which you want to remove the agent. Copy it in Note Pad, add the command line for each one and save the file as .cmd file. Each line should look like this:

psexec -d MachineName msiexec /x {25097770-2B1F-49F6-AB9D-1C708B96262A} /qn /norestart

or

psexec- d MachineName “msiexec /x {25097770-2B1F-49F6-AB9D-1C708B96262A} /qn /norestart”
Note: It has occcured a few time that putting ” ” gave an error.

Putting -d tells psexec not to wait for application to terminate. This is useful if you are running this for a very large number of machines. Otherwise it might take a long time to run on all servers.
Hope this helps!