What settings are preserved when hibernating and reviving Eon mode?

We had made some changes to an Eon mode database such as max ROS file size depot size. Some settings in CONFIGURATION_PARAMETERS were preserved but others were not, e.g. depot size. Is there some logic for what settings are saved to communal storage and what are reset? Also, customer thinks the MC settings were also reverted. Here is the customer report:
"The thresholds I set are now set back to the default after the cluster has been recreated.
I had all alerts enabled and now none are enabled. I have reenabled everything ..."