Are you using the merge tool before attempting to delete the objects? I can't imagine that happening, but I always explore every avenue!
Does the parent gameobject for each of your prefabs have a mesh or collider? This would cause the MAST Holder gameobject to be deleted. This may be on me if it's just a collider in the parent causing the issue. I've really only tested with mesh colliders in the children. If you use MAST tools Create Prefabs from Models, it will create more MAST-friendly models in the meantime.