Like the title says, I read some old guides to the game and people mentioned you could have too many saves in the old builds. I also remember being able to save over old saves but dont remember how to do it, am I misremebering?

The limit is 100 files (00-99). Nope, you cannot save onto existing files, only make new ones. You can delete the old files in the \saves\ directory or do it in-game.