Update: this problem seems to extend to any file that is automatically synchronized to iCloud. For instance, if my program updates a json file or if I edit any Python file, I have to kill Pythonista and restart it, I cannot just hit run (nothing happens if I just hit run). On my devices, CSV files are not synchronizing automatically to iCloud. If my program changes a Csv file, I can rerun the program without having to first kill and restart Pythonista.