It may "rough it up" a little, but the SJ stone is so soft, the affect would be short lived. I would also add that they don't consider the SJ stone as having "adjustable grit".
However, although the Tormek website says you can use the 1000 side to clean the SJ stone, Tormek in one of their online videos recommends not using it at all...
https://www.youtube.com/live/0htKSoTBjoI?si=QxZbSzyv_tyW__7d&t=3121
Instead, they suggest to use a scotchbrite pad, or as tgbto said, a rust eraser (which is what I use also.)
However, although the Tormek website says you can use the 1000 side to clean the SJ stone, Tormek in one of their online videos recommends not using it at all...
https://www.youtube.com/live/0htKSoTBjoI?si=QxZbSzyv_tyW__7d&t=3121
Instead, they suggest to use a scotchbrite pad, or as tgbto said, a rust eraser (which is what I use also.)