That's shouldn't be too much of an issue. You need to differentiate between host settings and vCenter Server settings. Networking (except for vDS), datastores, ... are host based whereas folders and permissions are vCenter Server based settings. So when you upgrade or reinstall a host, you'd usually migrate VM's to other hosts in the cluster (i.e. no changes to folders and permissions) and if you just upgrade the host rather than re-installing it you shoudln't even have to reconfigure the settings.
André