If you notice that SCOM is not properly discovering services on a particular server (e.g. it does not detect the presence of Exchange), you can resolve this by clearing the cache of the agent on the server. This will trigger a new full discovery, and the agent should now be able to detect the new services:

Log on the server of which services are not discovered properly.

Stop the agent (System Center Management service): net stop HealthService



Delete the contents of the Health Service State folder, located in the installation folder of the agent.
(default location: %PROGRAMFILES%\System Center Operations Manager\Agent).

Start the agent again (System Center Management service): net start  ...