Case: I wanted to reinstall the Enterprise Manager agent on a host. I went on to delete the host in the list of targets in EM. Then after a new installation and synchronization I somehow managed to push the list of targets from GC to the agent and thereby removing the host as a target in the local targets.xml file. Result: The monitored host did never show up in the target list of hosts even after a successful installation of the agent.
Solution: Create a temporary file /tmp/newtarget with one line:
<Target TYPE="host" NAME="foo42.bar.com"/>
Where foo42.bar.com is the host name. Then add the target with:
emctl config agent addtarget -f /tmp/newtarget