You have to try and clean up your project and remove extra files to get it to run as a browser game, there's a quick way to remove unused resources from your game folder here:
If after following this and creating a new save folder for your game you still can't upload your game, export a desktop windows build for your game and upload that. Make sure to explain the reason why you had to do that on the itch page in the description, so people/moderators know what happened.
But try to clean up the project folder first, because people are far less likely to play/rate a game they need to download.