The talk around it was vague but we did see him post-HW without his eyepatch in one scene when he was infiltrating a castrum with Krile - his left eye seems intact but the pupil had turned silver/white.

Now it's back to its normal colour without any acknowledgement that it changed.

(He's also had a haircut sometime between collapsing and reawakening... but at least that would have a more mundane explanation.)

Overall it looks like they might have just completely forgotten that Thancred's appearance throughout Shadowbringers doesn't match his physical body.