You need to stop and remove the container, then edit parameters and run again. Do not know how this implemented in Synology though. But if in the CLI, you need to stop and remove the container, then run a new one with all your parameters include changed ones.
I guess you need to remove the custom app and run it again. So, CLI would be likely better than GUI.
However, it may work to configure almost everything in config.yaml instead, but for example at least the STORAGE variable you need to provide empty in this case, e.g. -e STORAGE="", then it wouldn’t override what’s specified in the config file.