I do not remember if I had posted in this topic before (if I did was a long time ago).
In that chapter kaname say it's not the first time, and this can be related to him changing her clothes.
The first time when kaname changed her clothes was in first arc, after he turned back to her real nature.
Since we don't have any evidence that kaname changed her clothes more than twice we can assume he did it just in the first arc, and in the second one.
In the second arc yuuki did not wear any bra - if we are looking carefully at the picture it is obvious she isn't wearing one - the straps are missing. So we can assume that at that time kaname saw her bare upper body.
In the first arc we do not know if yuuki wears a bra or not, but how many women sleeps with a bra on? before being taken away by kaname and turned to that she really was she was resting/sleeping in her room and was wearing a nightgown, a different one from the one from second arc though.
i don't think they did it at all
because wouldn't she have become prego by now
because its now almost more than one year they lived so no way they did it
.i know i sound such an idiot with this comment.
Purebloods have a very low natality. for example haruka and juuri lived more than 3000 yrs but they had only two children - I doubt they were intimate only twice during those thousand of yrs.
If yume weren't intimate in that year which passed they can be in the near future