I would assume what would happen is Dusknoir LV.X would become a Stadium card if you chose to use the Ectoplasm power, but everything else would get discarded, since that is part of the Poke-Power's effect. If you didn't use Ectoplasm, then all Pokemon cards would return to your hand.
The thing is that Rescue Energy activates if your Pokemon 'is Knocked Out by damage from an attack', and Ectoplasm activates if Dusknoir 'would be Knocked Out by damage from an attack'. 'Would be knocked out'-related effects take place before 'is knocked out'-related ones.
Wait for another professor to agree/disagree with me though.