Because editing the Pro/PROGRAM is a manual process, Pro/E makes no assumptions about what you intended when you reorder items in the model tree.
Even if you had moved the hardware between the two subassemblies (if that were possible), it would have split the programming so that only the assemblies are controlled by the program.
I don't know of any way to make Pro/PROGRAM perform the way you are suggesting.
I would be very interested to know if you learn of a way to do this.