The problem with that is that you prevent the Itch app from automatically updating games.
Your players will have to download the entire game manually with each new version.
Viewing post in Fix trash in my board
For Pizberry it would seem they have a bunch of them that he doesnt need.
For myself i should probably look into that patching ability. Is that butler related? My download is less than 100mb right now so downloading the entire thing is not really an issue but if it grows patching in updates is a good idea.
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.