Once a system has been safely shut down, it can be restarted without repeating the configuration and first-time initialization process. If the system was not safely shut down, you cannot restart it but must start again with the configuration and start-up procedure (i.e., run legion_setup_state, etc.). In that case be sure to remove the $LEGION_OPR directory and to kill any extraneous Legion processes (use ps to check this).
Do not rerun legion_initialize. The objects created when you first ran it are still in the system, just in an inert state until the system is restarted. They will be reactivated and their state reloaded as necessary.