Deployment modes are an overlay on the base resource configuration defined in (generally) the 'core' resource collection:
You can copy resources from core to a deployment mode at any time, you'll just have to re-scan your config directory afterwards if you do it while the gateway is running.
But conceptually it's important to only copy the specific paths/resources you actually want to override in the deployment mode, not absolutely everything, or you're giving up most of the benefit of the inheritance cascade.