If you wanted to completely remove unused configurations in your mod, so It doesn't persist in the Config Editor on people that used your mod previous to that version, you can do the following:
// Do not bind unused property anymore.
// ConfigEntry<int> SpawnRateOverride = Config.Bind("Configuration", "Entity Spawn Rate", 10, "Description or whatever");
PropertyInfo orphanedEntriesProp = Config.GetType().GetProperty("OrphanedEntries", BindingFlags.NonPublic | BindingFlags.Instance);
var orphanedEntries = (Dictionary<ConfigDefinition, string>)orphanedEntriesProp.GetValue(Config, null);
orphanedEntries.Clear(); // Clear orphaned entries (Unbinded/Abandoned entries)
Config.Save(); // Save the config file
Quote from KittenJI on discord: