A.R.
Have you talk to his doctor about this behavior? There is a name (Trichotillomania) for compulsive hair pulling disorders.
I've attached a link to an information website about this issue.
http://www.trich.org/index.asp
I encourage you to read the information for friends and family and there is also a section for kids/teens to read. There are also support groups available which I think are so important so that he doesn't feel alone. I have a son with a learning disability and after years of researching, fighting the schools and other people's perceptions about my son alone I finally found a support group and it's changed our entire lives.
I had a friend who had Tricho and so did her mother. It is "like" a nervous habit but may be a reaction to an underlying depression or anxiety issue. Your son may not have much control over it, but you may be able to find some medical treatments or behavioral therapy that may help. He probably needs understanding and support more than anything right now. It's very difficult for people who have this disorder. They know they don't look normal without eyelashes or eyebrows and it can be so embarrassing for them. Sometimes that anxiety of looking different can increase their compulsion to pull their hair out making the problem worse.
I think there is a lot of hope that he will be able to modify his behavior. You mentioned that he does better when he wants to. That's typically the first step in changing a compulsive behavior but it takes work. Talk with him to figure out what he wants you to do if you see him pulling his eyelashes. Does he want a gentle reminder? Is there something else that might work better for him?
My son also sucked his thumb for a LONG time which is also an compulsive reaction to stress. He asked us for various help through the years but his compulsion was very strong. I thought school would change things but no one ever picked on him for it. Finally in 4th grade he asked me to have an orthodontist put in an appliance called a "rake" that literally stabbed him if he tried to suck his thumb. He was ready to change his behavior and I did let him make the final decision because the treatment seemed extreme to me. He had much success and was very happy with the result. Over time (he's 11 now) I've noticed when he's very stressed he's started sucking again at night but since he can control his behavior during the day he's still happy with the result.
I wish you the best of luck, and I hope you're able to post a follow-up response if you find something that works.