Can flour be used in processing some chocolates, and if so, how safe is that to include a gluten-free diet?

Yes, flour could be used in processing some chocolates, but FALCPA (the Food Allergen Labeling and Consumer Protection Act) says that all processing aids and ingredients that are allergens must be labeled. Manufacturers cannot use wheat flour on a candy line to prevent sticking without stating it as an ingredient. Be sure to read ingredient labels carefully or choose options that are labeled gluten-free in accordance with FDA regulations or, for additional assurance, that are GFCO third-party certified as gluten-free.