Maybe you need to disabled the data domain that you dont want to use, but when you enable again, you will need to restart the services.
Take a look at this:
(I dont know if in the new version, change something. Or look in the documentation 3.1)7
Let me know if this helped you.
I'm not sure you can control whether a dgraph process starts based on whether an application is using it, but could the new auto-idle function help you at all? You can configure data domains to become idle when they haven't been queried within a specified amount of time. They then become active again when needed for an application.
See Auto-idling and oversubscribing behavior of data domains in the Endeca Server Administrator's Guide.