During his absense Sherlock got knocked around quite a bit. As a result he has a mild brain injury which blurs his vision a bit, so ever since he came back he wears contacts, or glasses when his eyes are tired or irritated. John's never seen him with glasses before, so perhaps at first he thinks it's part of a disguise or something, but eventually the truth comes out and John learns about what Sherlock's been upto in those two years.