The problem isn't that he has files he doesn't need; it's that the devlog is showing him the change history (I assume Butler generates that automatically), and I haven't found a way to alter that history.
What you're doing isn't technically changing the version, but rather creating a new file and deleting the old one. That's why you see a clean history in the devlog, but the downside is that you're preventing the itch app from automating updates.