What should a person do who has separated from living with his father, who earns unlawful money, and the father wishes for him to return to live with him, knowing that he treats him well?

The Muslim is required to seek out the lawful in all their affairs. A son must return to his parents if they are in need of his cohabitation, as it does not appear that the unlawful predominates in the father's wealth. Eating from it is permissible or disliked with a tanzīhī disliking (dislike of avoidance, not prohibition). Honoring one's parents is obligatory. If they are not in need of his cohabitation, there is no objection to him remaining as he is, provided he sincerely advises and treats them well.