The workflow that you initially used to create a project is copied as a Workflow Template on the project. At that point, the Workflow Template is a completely separate entity from the original workflow. Any changes you make to the Workflow Template will have no effect on the original workflow. This allows you to use a workflow as a starting point and then customize the Workflow Template to the needs of your project. All the features, rules and settings available on Workflows can also be adjusted on the Workflow Template with except for the Project tab that controls project settings when a new project is created from a workflow.
See the Workflows page to learn more about creating and editing workflows.