The Phoebus Project is described as temporarily transfusing the copied brain-wave patterns of geniuses into whoever sits in the chair. It makes no mention of transferring intelligence from one individual to another, or removing it all together. So how, exactly, did Drakken become an idiot...erm, more of an idiot? There are a number of theories (machine malfunctioned, etc.), but overall it is a hole in the plot.