Are you using butler to upload the files? In that case you can rename the file itself before you upload it. If you are using the same Channel Name, Itch.io will still be able to mark this as the next version of the same file.
For anyone searching for this in the future. I deleted the build and reuploaded it with butler, it will then be named correctly. If people have downloaded the game with the Itch app, they will have to uninstall the game and install it anew. (re-install option does not work)