Root problem:
The only way epics currently disappear in plan mode is by marking them as "Done" (Epic Status field). If a user closes an epic using workflow transitions beforehand though, the epic is made read-only, so marking an epic as "Done" after that will fail.

Why we are where we are:
When we originally discussed how we wanted to mark epics as done, we decided to use a separate field so we we wouldn't have to handle workflows. A separate field gets around all these problems, so was a good solution for the problem. In case of the workflow option we would most likely have looked at the resolution field only. If there is a value => epic is done, if it is empty => epic isn't done yet. We could have set that field instead, but it would have been unclear which resolution to choose from, plus it possibly would have made the issue inconsistent with the workflow configured for it.

Proposed change:
I still believe using epic status is a good solution, but we could improve the current functionality by also applying the logic mentioned above. So, if EITHER the epic status is "Done" OR the epic has a resolution then we regard an epic as done. Had we implemented this logic upfront we could even have gotten around the upgrade task that tried filling in epic status values for already resolved issues