The post-it note will still be there regardless of your choices! It's baked into the default design of the menu screen lmao :3c Something does happen when you try to move it, though!
As for your problem: can I ask if there are any other game folders in your Ren'Py folder? I've (unfortunately) never seen this happen before, so I don't really know how to help T_T
Also, the updated game will still recognise and use your previous save files, though they might not work because I changed things around in the code. I think you might have 14DWY confused with another game, hehe ^^;