If Sasuke is fighting with Naruto & Naruto is hiding somewhere and fighting only with his clones, does the genjutsu of Sasuke has any impact on Naruto's Clone?
The Clone would be affected but will be destroyed soon after. we saw what happened to Kakashis clone when Itachi put it under genjutsu, inside the genjutsu the clone looked like a lifeless man made of paper and the tortures didn't work on it and it puffed out of existence very soon. I think the user of the clone would remember what happened to his clone but it doesn't affect him. besides Sasuke can find the location of the real Naruto with his rinnegan so there is no use in hiding behind a clone