However, baseball took its toll on Flick. Before the 1907 season, he considered retiring to pursue other business opportunities. By 1908, he developed stomach problems. Cleveland personnel initially said that the illness was related to Flick's overeating. He left training camp that year, complaining of "train sickness", and returned home to Cleveland. He missed the majority of the 1908 season, playing in only nine games. He missed the beginning of the 1909 season as well, as a doctor recommended Flick have his appendix removed. Now weighing , Flick was afraid of a bad outcome from the surgery, which was a significant risk at the time. He kept his appendix and played in 66 games, batting .255. He played in another 24 games in the 1910 season before he was again sidelined by his stomach ailment.