Shinnecock Hills is a Flynn course. While four greens are situated on the site of old Macdonald greens (the current 2nd,3rd,7th and 9th) they were all remodeled with the possible exception of 3. Billing records indicate that 3 was redesigned but either all of the green space indicated in the plans may have not been built or maintained for very long. Of those 4 green sites, the 2nd is a par 3 where Macdonald's 12th was a short par 5 playing from a slightly different direction (the approach shot was much different); the 3rd is played from tees on the left side of the 2nd green while Macdonald's played from the right side of the green. Three bunker sites were retained but significantly resized and reshaped. The 7th played from a different tee by Flynn, which is being restored as the Macdonald tee is the one currently in use. The 7th green was raised significantly and redesigned. The bunkering scheme for the 7th was entirely new. In fact, the Macdonald bunkering was completely different than other Redan bunkers looking more like Biarritz bunkers flanking the green. The 9th hole is played from tees by Flynn further back than the Macdonald tees. The Flynn green was saddled into the hillside while the Macdonald green was perched above the surrounding grade. Every other hole is completely original. Every hole is played from a Flynn tee to a Flynn green with only three hole corridors in common with the pre-existing design but with different bunkering.
I designate a Flynn design on courses where the overwhelming majority of design is Flynn. In the case of Shinnecock Hills, it is basically 100% Flynn. As for TCC, Brookline and Merion East, the courses are close to my threshold for designating them as Flynn courses. In the case of Merion East, Wilson was the man in charge for most of the changes, so I wouldn't presume that the changes were initiated by Flynn but rather through their unique working relationship. The changes after Wilson died can be attributed soley to Flynn. I am confident that the redesigns are Flynn (we have all the drawings) but the concepts cannot be limited to Flynn. So Merion stays a Wilson but to be more accurate, it can readily be thought of as a Wilson/Flynn design.
As for TCC in Brookline, 11 of the 27 holes are Flynn designs, at least until Cornish and then Jones did their work decades later. He redid nearly all of the greens and 90% of the bunkers on the course. Yet, I have not designated it a Flynn course for the list. It is arguable that it could be.
If Flynn came in and redesigned 9 existing holes and added 9 holes, I would typically designate that a Flynn design. Where Flynn made a few changes, it is not represented as a Flynn course but a rather a course with redesigns by Flynn. On such courses, I note the number of holes that are redesigns. In the body of the Flynn book, the details are presented.
Anyone is free to determine what is or is not a design or redesign. I assure you that the book contains enough detail for someone to decide for themselves.