Hey there,
I've identified a few bugs today, and this is one of them - you don't have to do anything, I'll release a fix in the coming week that will completely solve that issue.
I would still recommend putting save data somewhere else though - by putting it in the game folder, it'll get overwritten when the game updates (with the correct version, once this bug is fixed..), which may be bad for your players that want to hang on to their saves!