What should a son do if he is almost certain that his father is stealing subsidized flour from public funds?

If it becomes clear that your father is unlawfully consuming public funds, advise him with wisdom and good counsel. For "public funds are protected by Islamic law, and are even more sacred due to the multitude of rights attached to them," as the Prophet, peace and blessings be upon him, warned: "Indeed, some men delve into the money of Allah without right, and for them is the Fire on the Day of Resurrection."

As for the son benefiting from his father's mixed wealth, there is no sin in it according to the most preponderant opinion, especially if the lawful portion predominates. You mentioned that the suspicion of unlawfulness came from his selling subsidized material, and not all of his money is unlawful.