Thats an interesting philosophical question 
Is the cloned instancedmesh sourced from the clone, or the original mesh it was instanced from? At the moment it is option B, but i assume it would make sense, in that case, to allow changing the source mesh.
The clone function of instancedmesh generate a new instance from the current source mesh, which is the base of this issue. We could add a way to override the sourceMesh and define a new one when cloning. @Deltakosh , wondering what your thoughts are here, when you have the time