I am also having the same problem although my situation is a bit different. HQ server used to be on Box A. Well, I removed it from Box A, Box A is now dead, installed it on Box B and gave it the same IP address that it had on Box A. The IP didn't change, just the machine.
However, no agents are showing up in the autodiscovery for HQ server running on it's new box. I tried stopping and restarting the agent on a windows box but that didn't seem to work. Running "hq-agent.exe -setup" on the windows box where the agent is running didn't do anything or ask me if I wanted to regenerate tokens.
HQ server is running on an Ubuntu machine. I have a mix of agents, some of are running linux, some are running Windows. None have showed up since HQ was moved.
Is there some type of command that can be run on the server to contact all agents running on machines on your network and have them repopulate the dashboard again? How can I get all of these machines to show up in hyperic again without reinstalling the agent on every machine?