rather than punishing the behavior, have you tried rewarding for not doing it? Tell him that you want very much to help him overcome this habit and why (ex.cause not haveing eyelashes makes dust get in your eyes) You could make a sticker board and put the days of the week or even break it down further into hours, and for each day/hour he doesnt do it he gets a star and once he has a certain amount of stars he gets a special prize or toy he has been wanting, agreed on before hand. Could put a picture of the item on the board so he can visualize obtaining his prize with hard work overcoming his habit. Im assuming that he is capable of understanding a reward system. I would also make sure by asking him or taking him to the DR. that his eyes arent itching still.
Good luck, i know it must be difficult, wish i had more help to offer. Maybe somone else can give you better ideas.