After learning of the arrest of former governor Charles S. Morehead by federal authorities, Helm fled to Bowling Green, fearing his own arrest. Through the intervention of Warner Underwood he was able to return home on the condition that he swear an oath of allegiance to the Constitution. Nevertheless, federal soldiers repeatedly entered his home, encouraging his slaves to abandon him, and consuming or destroying his crops. Because the state's courts were closed on account of the war, he was unable to earn a living by practicing law. In short order, his once-substantial fortune was expended, and he resorted to borrowing money to support his family.