Did you perchance just add an autosave feature? The RPG Maker game Cube Dude's Farm had a similar issue with the game not saving that was tied to the autosave feature. The post no longer exists since they changed the comment section to a community forum, though I was able to find it in the recent posts on the author's profile page:
"Issue is related to autosave feature, I have re-scripted it and now it is working. Game will be autosaved on the actual slot"
No idea if this helps you at all. I will probably download the game like you suggested to be safe. Anyway, I do want to say that I am really enjoying the game and was having fun reading all the background lore and look forward to getting further into the story. Hopefully when I download, it will keep my save this time :)