@Guy-Gizmo said:

The whole point of me setting it up that way is that the actual logical structure of the data and the physical arrangement and implementation of it are conceptually completely separate. The latter is abstracted away by the interface of the former.

Then I think the cleanest solution is to have a tree (or w/e) that represents your logical structure, and that will abstract the whole physical layer. For a simple example you can look at the docs - the simple tree model.
You can put anything in that tree and it's basically your "data interface". It also shouldn't care that the physical nodes are destroyed as long as there's a logical node living. This way you don't have with model indexes and things getting destroyed in the background, because it's the middleman's responsibility. You should hover take care to notify the model when a node/leaf from the "logical structure" tree is destroyed (through the appropriate signals), so views can make proper adjustments.

I hope that helps somewhat.

Kind regards.

The dummy child is the culprit. It did not set the parent so the parent is invalid.