What is the ruling on the purity of cotton particles scattered from a machine that contaminates old cotton, and are these considered whispers (waswas) concerning purity?

Parts of cotton and its dust that reach you are considered pure as long as you are not certain of their impurity. The basic principle regarding all things is purity, and nothing is judged to be impure except with a sharia-compliant proof. We warn against falling into obsessive doubts (waswas), for the most effective cure for them is to ignore them and not pay attention to them.