I think its a pun like she "struck a chord" in his life.
Nothing is the same after she left, because she changed naota ie. He stops all the "nothing ever happens" monalouge, and keeps the guitar as a momento. I couldn't imagine him trowing it away.
After she flies away, he keeps haruka's guitar the same way he kept his brother's belongings. He was just as attached to haruko, so I assume he's doing the same thing, but when his room is shown he is outside talking with his classmates and the lights are off. It feels like those are things in the past which are important, but put away for right now because he is busy living in the present, or rather that he doesn't spend his time mulling over his memories, but thinks about them still.
Ex: Enjoying bad ramen and thinking about her pretty face...instead of sulking in his room wishing she'd come back.
Naota leaves the top bunk and all tasuku's stuff the way he left it out of reverance, and reminds him all the time. This leaves an empty spot in the room and in his heart. Haruka lays in his bed, and naota gets pissed and says no one is allowed to sleep there. Its obvious that the bed is kept empty for his brother's return, but later he doesn't seem to mind and even jumps up in the top bunk with her when his classmate comes over. I don't even think naota allowed himself on the top bunk until haruko came along putting her in a special place.