Okay so when I chop down a bush, and leave the room, and then come back, the bush is still chopped down. That issue is solved when I make the room not persistent, however when i re-enter the room, there are two Links!! One where I set him to begin the game, and one where I set him to go to when he leaves the other room. Sorry, my programming skills aren't exactly topnotch.
I'm trying to learn though.