Sorry to necropost, but I just started having this issue after trying out the Pythonista Beta. I tried reverting to the standard app store version, and the suggestions above, without success. I can see the Pythonista folder in iCloud from the files app, and from my mac. I can even create new scripts from Pythonista which will save in iCloud, but Pythonista cannot see them for some reason. Any ideas on what I can try?