Splunk Support gave me the correct answer. Rolling restart of the SHC resets the confgurations, so you no longer see the system level configs in the UI.
Actually, it is not necessary to perform a rolling restart of the entire cluster. You merely need to restart the instance(s) on which you previously exposed the system settings (via the "Show All Settings button).
The system-level settings will only appear on those instances where you clicked "Show All Settings."
Presumably that's because you're accessing the cluster members from a load balancer. To determine the instance, the best approach would be to log into the members directly.
On the other hand, you can do as you did, which was to restart all instances. But it seems unnecessarily inconvenient to restart them all, when restarting just one would handle the need.