 Robert assessed his financial losses during this period amounted to £51 10s.Like many Protestants he joined Murrough O'Brien, 1st Earl of Inchiquin to fight the Confederates and by September 1646 he had risen to the rank of lieutenant-colonel in the regiment of Richard Townshend.In February 1648 he was arrested, with three other officers, for refusing to join the royalist rising under Inchiquin.