You will have to update the config file and restart the Sync Gateway for database changes to be persistent . If you want to do it without downtime, then in addition to updating via the admin API (which is not persisted), you will also have to update the corresponding config file so the changes are consistently applied on restart. Note that the config changes applied via are scoped to that sync gateway .
I am curious about your use case. Unlike users for instance which are fairly dynamic, database config rarely change. What specific database config properties do you expect to update and how often?