One of the more common alerts that I see in SCOM environments is the ‘Health Service Heartbeat Failure’. All too often it is still possible to ping the system, and yet the heartbeat alert remains. The typical fix is to simply stop the health service on the problem system, delete the contents of the Health Service State folder for the agent, and to restart the service. In most cases this resolves the issue. Since this is such a common occurrence I decided to create a runbook in System Center Orchestrator to automate the fix. In order for this to work it is necessary to be running System Center Operations Manager and Orchestrator 2012 and to have the SC 2012 Operations Manager Integration pack installed in Orchestrator. Note: this will not resolve any actual problems with failing heartbeats, it will simply clear the cache and force the agent to attempt to update policy.
For testing I would make sure you have a current Heartbeat Alert and set the resolution state to something other than new or manually stop the service on an agent system. Make sure to start the runbook and set the heartbeat alert resolution state to new. Monitor the runbook, the alert, and the SCOM Agent to ensure the process works as expected. Good luck and I hope this helps with your re-occurring Heartbeat Alerts.