I see here serious misunderstandings of the book (unfortunately also in previous answer).
The essence of "Algernon–Gordon Effect" was that the effects of the procedure, that they both underwent, are strictly temporary. Just as their intelligence was raised, it had to go down. When his intelligence was declining, Gordon was afraid of losing his ability to read, but his fear wasn't rational.
In "Flowers for Algernon" the experiment with raising intelligence is just a starting point for exploration many themes. One is relationship between people having both low and high intelligence and others, how genius or disability alienates them from "normal" people. Charlie's IQ raises a wall between him and Alice when it's high just as well as when it's low. Naive simpleton turns into arrogant genius, just as unhappy as he was before. Instead of joy, high IQ brings him disappointment and disillusion.
Another theme is dichotomy between emotional and intellectual development. While Charlie's intellectual development was undone, his emotional (and, yes, also sexual) development was not. He had serious problems because of his parents' misunderstanding his relationship with his sister. Experiment with raising the IQ had only a very limited success, but it became an opportunity for Gordon to overcome his deep-seated emotional problems and to finally mature and become a man able to decide of himself, live his life according to his own will, and overcome his complex of inferiority associated with IQ.
All in all, I think that Charlie didn't lose anything in terms of intelligence, but gained a lot thanks to his maturation and emotional development.
Charlie is a winner, but other characters are not. Algernon didn't cope with tremendous loss of mental capacity, he shows what could happen also with Charlie, if not for all his development. Alice also couldn't cope with what happened to her lover, otherwise, with Charlie's newly gained maturity, their relationship might still have flourished.