I agree with Jim and Tom Paul,
Mill Road Farm GC would certainly be one of these for me. It looked to be a fascinating design. Flynn's mandate was to build one of the hardest courses in the country. His 7000 yard par 70/71 course in 1926 did that with angles and bunkering that may have been enjoyable difficulty with a nod to difficulty.
Tommy Armour was the only professional to break par at MRF, he did so in 1934 and won the $500 standing offer to anyone who could do so. Armour played the course in 69 strokes to break par of 70. He took 40 minutes to play the 18th in bogey to accomplish the feat. For a comparison in difficulty, in 1940, the CDGA rated MRF at 76.32 vs. par of 70 and Medinah #3 at 76.08 vs. a par of 72.
Flynn's
Boca Raton South was probably another top 10 course in the country at the time. Interestingly, Tommy Armour has a history at both BRS and MRF. Of BRS, Armour said to Grantland Rice, "I am going to show you one of the finest golf courses in the country...Not in the South only--in the entire United States. At least it is as fine and as fair a test of golf as I have seen anywhere."
Opa Locka GC is another Florida course by Flynn that would have been a great addition to golf in that state and beyond. It was the centerpiece of Glenn Curtiss's planned city of Opa Locka that crumbled under the combined weight of a real estate bubble burst and a devastating hurricane. The design was amazing. Here is an example of Flynn's 6th hole:
I would be satisfied with these three, however I would also add
Lido (sorry) and one of Devereaux Emmet's NY courses that was lost in the expansion of NYC. What might of been Emmet's greatest lost course?