Whenever you start a container which uses a standalone configuration, Cargo will delete the configuration directory in order to reinstall a clean standalone configuration. Thus all deployables that would have been previously deployed to this configuration will be removed. Of course, they will be deployed again if you have added them to the configuration (see Static Deployment). The reason for this behavior is reproducibility which is for example very useful for automated testing. If you wanted to keep a generated configuration you could ask Cargo to generate a standalone configuration once and then consider it an existing configuration.
There are different ways of using a standalone configuration: