Hello ! I'm not sure I understood correctly so lemme know if I'm missing the plot.
- If your issue is that both the old version and updated one are visible on your game page, you can just hide the previous one.
- if you're releasing a standalone version of your game (i.e. a zip file) then yes players might have to download the new version each time it's released, however if you'd like the old game files to be overwritten I'd advise you to create an installer (using inno setup for example) which will allow you to leave the user config intact upon installation while simultaneously updating the game's executable and/or resources.