Flanagan's reputation gradually grew after he moved on from being primarily an accompanist: in a 1992 article, critic Leonard Feather suggested that "Flanagan is the pianist most likely to be named a personal idol by other jazz pianists, whether they be swing veterans or avant-gardists". This made him more in demand; the workload may have contributed to his collapse in 1991 and subsequent quadruple bypass heart surgery. He returned to playing within weeks, but also returned to hospital for treatment for an aneurysm. Flanagan was awarded the Danish Jazzpar Prize in 1993. Three years later, he was selected for a National Endowment for the Arts Jazz Masters Fellowship. In 1990, 1993 and 1997, Flanagan toured Japan, where he was very popular, with 100 Golden Fingers, a 10-pianist group.