So here's the EMH holding a chunk of 7's head as he fiddles with a Borg tech implant in Timeless. He has dug this chunk out of the presumably now defrosted 7.. maybe she wasn't defrosted when he started sawing up her face which would make it easier to cut precisely but he's been at it for a while now so this chunk of 7's face is definitely defrosted. In fact upon close inspection it appears that we are looking at bone, metal, techno thing and eye. So he may well have scraped all the flesh off the better to work with but the eye is still there!
The eye must be a prosthetic one. Is her other one prosthetic? Is that why Borg vision is so twisty? Why would the Borg bother with stuff like eye color? Why would they bother matching it to her other eye? Is this why 7's eyes are so big, because they are prosthetics?