that jerry's world doesn't revolve around nor is truly shaped by the system, so he has to stop being so fixated on it! focusing so much on the system and its prompts means he is letting himself be controlled by it, the very thing he's been wanting to avoid.
from the very beginning, he only thought of them as characters whose emotions and actions are predetermined by the system, but later in the story, he realizes that was a mistake and that these are very real people that he shouldn't be afraid of just because of the system windows and statuses.
he spent so much time being fearful of going down these predetermined romance routes that he became completely blind to the fact that so much was already different from the fictional storylines he knew.
the end of chapter 56 is where jerry begins to understand this! he realizes that the system won't make his brothers have incestual feelings for him; he just has to honestly accept their pure brotherly love and express his in turn. in doing so, the system acknowledges this and completely erases the mere option of the remaining incest routes, making jerry finally comfortable with his sibling relationships.
of course, jerry doesn't completely discard his preconceived notions of the system's connection to his world after that. the beginning of chapter 60 is definitely the true turning point of his attitude towards his situation. thanks to ilya emphasizing jerry's free will and choice, jerry realizes that being so anxious about the system's romance prompts all the time is ridiculous, rejecting its route and deciding to make his own choice when it comes to his relationship with ilya.
the system is only a tiny reflection of reality based in the original content separate from jerry. it was never the master of his fate, nor the fates of those around him!

I came back to reread this manhwa today because of how cute it is!
Also, I don't like getting into fights, but... wow. Let's just say I'm a bit shocked by the lack of reading comprehension exhibited by some people who completely miss the main point of this story.