There are two ways to remove an object from the InstanceRegistry. The first, and most automatic, is for it's reference count to reach 0. When an object is destroyed it is automatically removed from the InstanceRegistry.
The other way to remove an object is to call removeInstance[ByString] or removeInstance[ByClass]. These will remove the objects from the registry without destroying them. They do not addRef however. So, if you create an object, insert it into the InstanceRegistry, remove it from the InstanceRegistry and then deleteRef it, it will be destroyed. (Assuming no one else as addRef'd it in the meantime.)