How can I re-order or delete the pipeline stage once I have added a pipeline?

Once you add a pipeline to a project/opportunity, you cannot edit the pipeline (i.e., re-order stages or delete stages) that has been added.

However, you can go to Daylite > Preferences, select Pipelines, and make changes to the pipeline. These changes will be reflected when you create new projects/opportunities and add the pipeline (previous projects with that pipeline will not reflect the new changes).