If that's when investigating all 3 groups, 1 small reference to a threesome in Book Two will be the same. But before the last scene, you can choose whether to continue with all 3 groups and throuples or choose one.Yes it is a bit confusing for me too, in the end of book 1 I made 3 saves, 1 for each threesome variation but in all of them when loading to book 2 and playing it they all act like the choice of threesome was with Zem and Nia. Downloading again the book 1 to install unmodded and then load the 3 saves again and play in book 2 to see if reflect the choices. Probably better I put URM too so I can track the variables.
FYI I played and the end of book 1 persistent save were made with the current book 1 mod and the GOG version. I had those saves done with the other version but doesn't seem it matters, in the 2 variations where Sylvia was in the threesome they still act like it was Zem and Nia chosen. It is weird or maybe I'm missing something.