Flynn's commercial recordings include Tchaikovsky's "Swan Lake" (published by the Royal New Zealand Ballet), "Hair", three versions of "Jesus Christ Superstar" (two as conductor and the third as music director), and two versions of "Ned Kelly", for which he composed the music. He arranged and conducted music for a film promoting North Carolina. His arrangements of Ludwig Minkus' score for "Don Quixote" ("Kitri's Wedding") are heard in a DVD of the American Ballet Theatre's telecast of the ballet for PBS (Kultur). He conducted for Kiri Te Kanawa's film debut in New Zealand ("Don't Let It Get You") and for Marjorie Lawrence's last commercial recording "Waltzing Matilda", with the Sydney Symphony Orchestra.