So the "university scene" happens two years after Natsuki disappeared from Yuni?

Two years after high school.

In my understanding, they meet up 2 year later..

Yes. And now Yuni is a second year and Nat-chan is a 1st year. Since they were 1 year apart in age. He took that chance!!

For 2 years being joyful, it feels like a short while. But..
2 years being sorrowful alone.. that must feel like such a longggg time, especially they used to be together all the time.