Please try reloading the save file with Force Recovery Mode enabled, which would bring you back to the start of Day 3 chapter. You'd have to replay the portions from start of Day 3 leading up to the route branch, but I'm fairly certain that it should fix the problem you're having which is due to incompatibility of old saves. The save point you made for the save file is after where I added new code to fix an issue where players are softblocked from progression by saying No to every single love interest, which affects how the No option is displayed during the route branching for the last love interest to respond to.
Please let me know after trying that to see if it works. I apologize for the issues. Thank you for playing Emberfate!