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so we've all acknowledged that in series 1, Crowley wears glasses around everyone else (including Aziraphale!) because he's not comfortable with people seeing his eyes
and then in series 2, he makes a point of taking off his glasses in the shop, showing how he's comfortable around Aziraphale.
but it's not just that! Crowley's eyes reflect his demon status, and he's become comfortable being a demon around Aziraphale, because they're on the same side now.
and at the end, when Aziraphale rejects him, and establishes that in his mind, demons=bad, and Crowley's good because he's still an angel deep down, Crowley puts the glass back on. Not only to put the emotional barrier/safety net back on, but to hide his demon-ness once again. Because he's no longer comfortable being a demon in front of Aziraphale.