I mean the premise of the "Long Distance Relationship" in Japan of all places was pretty silly at best. I know Japan likes to pretend they are just like some of the bigger countries in the world but the total size including it's major islands is still only about the size of California. Any "distance" could be covered by a 1-2 hour train ride and if you limited it to just the weekends (or every other if you want to be real conservative) it wouldn't be too cost prohibitive either. Not to mention as Taku mentioned it's only 3 months, hardly a death knell for a relationship though it does suck it would have happened right as they finally started officially dating.
I don't know, I just find it adorable that Japan tries to use these types of scenarios to create drama when they still live on their tiny little island nation and it just really shows a lack of perspective. Some authors usually fix this by having the LIs randomly decide to study abroad (as if that was just a totally normal thing) but it still shows up pretty frequently where all they do is move prefectures and they act like they'll never see them again. Like bitch, you have a nation wide public transit system that has really good infrastructure. You aren't far from ANYTHING in Japan at any given moment let alone someone you want to bone.