Update README.md

Future rebuilds should use the flake, not configuration.nix

Author: JillThornhill

README.md

@@ -199,6 +199,15 @@ Note that this command references the URL of your flake, in this case `.#`,
 together with the name of the system `hetzner-cloud`, as highlighted by the
 comment in the sample flake.
 
+This will configure and build the new NixOS server. Since the configurations are defined
+in the flake, it will not create `/etc/nixos/configuration.nix`. If you need to make 
+changes to the configuration in future, you should make the changes in the flake, and 
+rebuild using the --flake option as shown below:
+
+```
+nixos-rebuild --flake <flake URL> switch
+```
+
 The [Quickstart Guide](./docs/quickstart.md) gives more information on how to
 run **nixos-anywhere** in its simplest form. For more specific instructions to
 suit individual requirements, see the [How To Guide](./docs/howtos.md).