Pat,
My understanding, it may be wrong, is that there is no holes nor common ground in the current South course. There may be some ground on the current North course but there is no surviving Flynn holes. As you say, the best way to determine this is with an aerial of the current courses.
Craig,
Dan Wexler notes in his books of lost courses that both Boca Raton South and Mill Road Farm Golf Course were considered one of the top courses in the country. This is corroborated in contemporary newspaper and magazine accounts. There are a number of other NLE Flynn courses such as Opa Locka, Floranada, and Yorktown CC that, if around today, would add to the consideration and regard for Flynn's design work.