I'm trying to upload a new version of an HTML5 game I'm working on, but I'm encountering a strange issue.

When I delete the file for the current game, and upload the file for the new version, the save data from the old file will somehow show up in the new one.

This won't happen if I access the secret link in a private browser window (i.e. incognito mode) .  However, clearing cache and cookies for itch.io in the regular browser still leaves the old save data.

Wondering how this even happens in the first place and how to stop it.

I never experienced it, just read about a similar case/textline when uploading a game, it says a feature referring to "updating just the new lines only". Maybe you've checkboxed this option there and that's why it appeared in that case?

This depends on the game engine you’re using. All HTML5 games are hosted on the same domain, but new uploads are placed new new sub-directories. Most game engines use local storage for save files, so it’s up to the engine to determine how they scope the save game data.