MarcH. That is exactly how I sharpened my carving knife. The problem was not that the stones would hit the vise. It was that the Martef coated knife would slightly move despite of the real leather chamois. I have not had this problem with knifes without this type of slippery coating.
Lay: try using the aluminum foil tape that is made for sealing heating and air conditioning vent ducting. It seems to stick to everything, allows the vise to “bite” into it for solid positioning and still comes off without living almost any adhesive behind.