It happens to me with both versions, too. I have the itch.io version and the Patreon version. With both, I always have to start completely from scratch whenever I take a break. There’s a small screenshot in the load menu showing that it is saving correctly, since it displays more than 5 gold.
Is there any way I can send you a save file? There is a file named "1-1-LT1.save," which likely corresponds to the manual saves. But there are also files ranging from "auto-1-LT1.save" to "auto-20-LT1.save," even though the game doesn't actually have an auto-save feature, right?