Begin with a workflow in JIRA that is already associated with a project.

Copy that workflow and give it a new name. Create a new workflow scheme and associate the new workflow with that scheme. Create a new project and assign the new workflow scheme to it.

Make three changes to the new workflow:

1) Modify status, for instance change Open to ToDo
2) Modify transition, for instance change Start Progress to Begin Work
3) Associate the new workflow with a different set of issue types than the original workflow

Despite these changes being made to a copy that is associated with a different scheme and a different project, the original workflow will pick up at least some of the changes to statuses, but not to transitions or issue types.

The reverse is true as well. I had this happen accidentally this morning when I created a copy of an existing workflow and ran through the above. When it was brought to my attention, I went to fix the original workflow, only to discover that in the Administration -> Workflows view, the original workflow still looked fine and matched what was expected. Through that view, it had not been edited. The timestamp of the last edit had also not been updated. When viewing the original workflow through the project to which it was attached, however, the changes were visible. This despite no changes having been published to any workflow, including the copy.

You cannot directly edit a workflow through a Project -> Administration view, but I got to it through the workflow scheme and reverted the changes on the original workflow. I then checked my copy and saw that the copied workflow had the statuses changed, but the additional status I'd created, as well as the transitions I'd modified, were still there.

It looks like a copied workflow continues to reference the same database rows/columns for statuses despite referencing new/different rows/columns for transitions. I would expect a copy to be completely autonomous of the original.