I'm not positive, but I think that the name of the .zip file doesn't matter, and that this is happening because the .zip contains a folder at the top level. In each version, the folder is named differently, so when the client goes to install the contents of the .zip, it thinks that the folder is something brand-new and installs it alongside the existing ones. So, I think that if you either keep the folder names inside the .zip the same for each release (e.g. just "Weird and Unfortunate"), or if you just zip all the files directly instead of zipping a folder, then Itch will understand that the new version should go on top of the old one.