I like to imagine Koishi still has a conscious mind in her brain, and that closing her third eye only severed it's connection to everything else. Meaning the original version of Koishi is still in there, still thinking and seeing the world around it, trapped in her own unconscious body.
It just kind of adds to the tragic aspects I really like about Koishi.
I'm still a new fan so I haven't consumed enough fanon to know if this is common or even really considered? But I also haven't consumed enough canon to know if anything contradicts it.