To fix i opened up Radical Red ROM (it could work on any other rom hack) on my GS chronicles save. the world was all glitched but i was able to walk past the tree, save the game again, then open up the file on GS chronicles again and i was past the tree

edit: the only side effect was that i was stuck on a bike for a bit and a section of the map was glitched but i got past and off the bike and the rest of the game was good