During the attack of conjunctivitis
, you might have had superficial punctate keratitis
which has probably not healed so far and causing the problem in using the contact lenses. You should get your eyes examined with a slit lamp to know the status of your cornea
before using the contact lenses.
Meanwhile, you are advised to use glasses instead of contact lenses. Also, using some lubricating eye drops 3-4 times a day will help.