Good question! I tried from a fresh game, but unfortunately get the same error. That said, I'm not familiar with Ren'Py or how Itch.io does updates; is it possible there are some other settings/files left over from the previous version aside from save files? Happy to try a reinstall from scratch…
Quick update, however: reading the code, I could see you use a different object (persistent) if Files is accessed from the main menu. I gave it a try and that works just fine. Though I can't see some documents I expected, e.g. the testimonies from the trial that you find/are given; unsure if those are specific to the save or just stored somewhere else.
(Also, totally separate—the proofreading you did for this game is exceptional, so in several thousand words of text I only found a couple of really minor typos. Early on, looking for the wine: "Off to the side, there's a glass case containing a a jagged purple rock…". And after your little wrestling match: "MC: Hello, he-who-stil-won't-use-my-name.")