The docs at the end of this page give a warning that auto paths aren't removed from the rio ever by default. It only ever adds or updates files. So, when the auto builder automatically grabs all autos in that folder, it will also continue to grab old ones.
We should make a gradle tasks that ssh's into the rio and removes old paths. https://docs.wpilib.org/en/stable/docs/software/roborio-info/roborio-ssh.html