Solid Editing - Cylinders used to subtract from main Object re-appear

[tshum]

I've built a simple solid composite using two boxes and two cylinders, then unioned them into a composite. The History is set to Record. After I grip edit an edge using the move grip tool, the edited solid appears correctly, but the two cylinders used to subtract from the main object appear as part of the composite.

I know that after editing subobjects of a solid, the solid history is deleted, but why do the cylinders become visible? Is this because the history of their Boolean subtraction is also deleted?

File is attached.