Share the subfolder separately from A or B.
I’m assuming this is a separate copy of the data compared to what is on C and the dual booting part is irrelevant apart from the fact that both C and D can’t be online at the same time.
If, on the other hand, you’re trying to share some of the data between C and D on a common partition but have them as different Syncthing installations with different configs, do not. You will not accomplish this without messing things up.