I'm not sure if that will work though since potentially I'll need to add or remove vertices from the list entirely. Like if an area is even and a dig a square hole into it that's 4 extra faces.
Yeah, changing the topology of the mesh will break the hierarchy. It might be possible to include the degenerate face triangles in the original mesh so the topology never changes, but I can't say for sure off the top of my head how the collision system would behave with that kind of degenerate geometry.
Perhaps I could just manage a list of triangle entities directly? Or maybe a list of ConvexHull?
It might work. Having a massive number of triangles hanging out in the broadphase isn't ideal, but you could give it a shot and see if it can handle it. A list of ConvexHulls might work too; I'd use whichever feels more natural. ConvexHulls in v0.14.3 and before might have a slow startup time.
However, triangles allow you to force collisions to use their normals which would help prevent bumps when things slide across a flat triangulated plane. ConvexHulls have no such feature, and would likely cause noticeable bumps when trying to slide across borders.
The 'best' solution to this problem would be something currently on the to-do list. In the late stages of v0.15.0 or possibly a little after its release, a new dynamic acceleration structure is planned that can handle changes to mesh topology without having to do a big rebuild process. The initial structure construction phase will be a lot faster too.