I believe this was the reason why his eyes were so important. Harry's eyes were what kept Snape going, because he could always see a bit of Lily within Harry even though most of him was like James. It must have been so fustrating for Snape because Harry was Lily's child who he loved but was always James's child whom he hated. It must have been a constant battle inside his heart, but I think the colour of Harry's eyes always helped him remember Lily and remember what he was doing for her by protecting her child.
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