Before stopping the Directory Server or shutting the machine down, you should stop all enterprise server instances that are running. When you stop the Directory Server using Enterprise Server Administration, there is an option to stop all servers first.
On system restart, unless Restore Servers on Startup on the Configure Options page is checked, the Directory Server does not automatically start any enterprise server instances that were not stopped before shutdown (and so are still marked as "Started" in the Directory Server repository). If the Server Monitor is enabled on the Configure Options page it will check whether these enterprise server instances are still active, and will mark them as "Not Responding" in the Enterprise Server Administration servers table on the Home page. Each enterprise server instance will then need to be restarted manually. You can do this by clicking Details and then clicking Start Server for each server.
If Restore Servers on Startup is selected, when Directory Server is restarted, it reads the list of servers that were previously marked as started, checks to see if they are running, and if not, attempts to restart them.