It should not be a problem of the save. You can try starting every dialogue and instantly skipping. That will reset everything to default, so then you can redo the choices. It should work like that.
I tried skipping every dialogue to reset then remaking choices several time on a couple characters and still was only able to see one ending for each character. I tried different combinations of choices that left the attitude at "Dislike", "Indifferent" and "Adore" but it would always play the same ending. I tried both on Braga and Vionne if that helps.
I tried with both Airi and Isabella, and still only one ending on both. Unrelated but also with Airi I wasn't ever able to achieve "Adores" status. I think whatever is the good option in the Lonely Confidence story isn't granting enough points to reach the maximum. With Isabella I tried different levels and same ending every time.
Shot in the dark but is it possible the wrong build got uploaded? I noticed that the last modified date of the executable is about 2 hours before I reported the bug.