We note that Algernon, the rat, died and that seems to indicate that the procedure not only wore off but had some severe after-effects. Charley Gordon did not die but was it suggested that he was left with a more severe deficit in the end?
EDIT: If the rat's death meant that the procedure had injured the rat in some way, the death being a consequence of the procedure causing decline below whatever the rat had been, it seems like the diary would show somehow that Charley was less intelligent than pre-procedure Charley. I vaguely remember that he had forgotten something he had known before. He had made arrangements to move to a group home or something whereas before the procedure he was living on his own in a rooming house so doesn't that suggest he had lost some skills?