Everything in the DB will be 'moved'. Make sure you look in the database after installing 9.5 to check the Keyvalue table for references to the old server name. Same goes for Agents.
Use the CoreDataMigration.exe in the Management Suite map on the new server to connect to the old server and migrate everything 'file-system based'.
Please check good for references to the old server, or isolate the old server and create a DNS alias with the old server name pointing to the new server
Frank