Certainly, as Mike Cirba said, Flynn worked on Lancaster and Merion for more than 25 years each. He gave a lot of his efforts to these two courses. He also worked on Cascades for many years. He and his wife loved vacationing at the Homestead--it was a very special place for them. His efforts to improve that golf course over 10 years or so were significant. I think Flynn cared very much for the Philadelphia courses. He lived in the area and his friends were members of his clubs. I know from Flynn's daughter that he was very fond of Philadelphia Country Club. He improved the course greatly, especially prior to the 1939 Open. I believe some of the work that was credited to Maxwell was really Maxwell implementing Flynn's plans...without question that was the case of the current 10th hole.
Yet, Flynn would have well understood the significance of Shinnecock Hills and more than likely knew that was his undisputed masterpiece. Too bad so few over the years knew what was Flynn (all of it) and what role Dick Wilson played (zero design) and Howard Toomey (never did any design work though is often given co-billing).