I'm not really sure what you want to tell me here.
I remember that I did the "training" of the sister (or rather I used CTRL during her training and only did what was strictly necessary and nothing more) After that I went to do a couple of things, but I'm not sure what, since I used CTRL to skip those parts. My intention is only to do what is strictly necessary to advance the main story and that of the sister. In fact, that's what I've been doing up until now, and I don't see any reason to change that approach.