When a young computer prodigy discovers he exists in a virtual world, he reprograms reality to save his father with cataclysmic consequences.

The most recent draft of the logline is too long and includes too much redundant detail. What is the specific plot beats you need to make this story work?
Inciting incident is the discovery of living in a computer generated world.
The goal is to either live with his parents again then is is to save the world.

I think saving the world is a bigger stake and therefor think it would make for a better goal. As such the inciting incident needs to instigate him to need to save the world. Perhaps all of humanity live happily in a computer and are fully aware of it to. Then the inciting incident can be his discovery that the digital universe he lives in is falling apart and as a result needs to take action.

Your logline is too complicated. It makes my brain hurt. Just state the thread of the story.

After an orphaned computer geek loses his parents, he tries to bring them back to life using complicated mumbo-jumbo.

Hope that helps.

From reading your comment I feel like the original logline almost has 2 inciting incidents.
It seems that the reprogramming of reality should be the inciting incident which leads to the goal of trying to fix what went wrong and save their reality.