Ok, so Using JPD the Hierarchy does not work quite the same. So what I am looking for is.
I want all the Issues (stories or epics) containing the link type Implements where the linked story is not in Status - backlog or status category - done.
Given any of those results are epics, also return all the children of the epics.
I don't believe there is a way to do this with built in JQL but if there is an marketplace app, I would be happy to explore. If your recommending a marketplace app, please also include how you would use that app to accomplish not just "this app can do that". I have been trying a few and not been able to solve it yet.