I have recently seen many different uses of the agent "Repair…" action when it comes to agent install and upgrade. I have put together the following information with the help of the setup team to guide you on the uses of the repair action.
When running agent repair the system basically does a reinstall of the agent using the default action account that was specified during initial install (local system in most cases). Also, if the agent was removed manually from the server, but still present on the console in a "Grayed out" state, using agent repair will cause the agent's health service not to start because it does not know the default action account to use due to being previously uninstalled.
If you were using the AD Integration feature, the agent behavior will be changed back to being managed via the RMS, no longer using AD Integration.
Full details can be found on the OpsManJam Web site.