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A habanero chili has as its active (or caustic) ingredient a chemical called capsaicin. When the eye is exposed to this chemical in significant concentrations it can be quite dangerous to the eyes. I don't know the approximate concentration of capsaicin in an individual habanero chili, however, even a little may cause some significant symptoms.
A corneal abrasion, significant conjunctivitis, intraocular inflammation called uveitis (aka iritis) or inflammation of the eyelids called blepharitis can all result from this exposure. My recommendation is to flush the eye continuously for at least 15 minutes with cold water, moving the upper and lower eyelids up and down to make sure the water gets underneath them. It sounds like you've done this. I would make sure he's out of his contact lenses for the next several days and he should get a new pair to put back in when he's ready to go in them again (which probably shouldn't be until the eye looks and feels normal).
It is possible that he can have long term eye problems in the way of light-sensitivity and discomfort that can accompany several types of chemical exposures to the eyes.
for that reason, if he is still having significant symptoms (either pain, light-sensitivity, or decreased vision), then he should be seen by his eye doctor as soon as possible. Artificial tears and lubricating eye ointment can be purchased OTC at your local drug store and used to help with the pain while trying to get into the eye doctor's office. Cool compresses can also help his symptoms.
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My opinion is solely informative and does not constitute a formal medical opinion or recommendation. For a formal medical opinion and/or recommendation you must see an eye doctor.