The saving system is built directly into the Ren'Py engine and doesn't give me much control. Based on my research, external software like OneDrive or even certain antivirus programs can interfere with save files. The default system is frustrating, so, for my next games, I'm planning to either write a custom saving system for Ren'Py myself or move the project to another engine like Godot.
If you have a broken save file you'd like me to investigate, please upload it to GoFile (or another file hosting site) and send me the link on Patreon or Discord. I'll gladly take a look, but I strongly suspect the issue is either system related or caused by external software, since saving works perfectly for me across multiple devices