On the Beast's Lair forum post about the Fate/Stay Night Realta Nua PC English Patch, there is this item in the FAQ:
Q: I want to view the original 2004 version of the relationship between Sakura and Shinji, but I don't want to view the H scenes, what can I do?
A: We're working on something to accomodate this request. In the meantime you need H scenes on to view the original version of the Shinji/Sakura relationship. If you don't want to view the H scenes but want to see thier original relationship, then my advice would be to, starting from Day 5 of HF, turn H scenes on when Shinji is in a scene or is mentioned, and on Day 14 make sure you have H scenes on until you see the last Shinji scene.
This can also been seen in this link.
Now i am assuming that what it's talking about is that in Realta Nua, Shinji's and Sakura's relationship is different compared to the original game. In the original Fate/Stay Night their relationship was that Sakura would became the new head of the Matou family, which Shinji believed he was entitled to, and when Sakura felt sorry for him, Shinji thought she was submitting to him which lead to years of physical and sexual abuse.
This leads to Heaven's Feel where Shinji attempts to rape Sakura, threatening her that he'll tell Shirou about what he has being doing to her and claiming that Shirou won't want to have anything to do with her after that. Sakura snaps and kills Shinji and then realizes she's the Shadow.
However, when I played it, there was no depiction of rape so I can't understand how or why Shinji's and Sakura's relationship would be different in Realta Nua. How is their relationship different, and why would it be changed? If Sakura's sexual abuse is cut out from Realta Nua does this mean her abuse at the hands of Zouken and his worms is also altered, and if so, how?