Well, I think that yes there are at least partial solutions that would help. But from what you wrote in your reply, it sounds like itch does not keep backups of the all the files that developers upload to their projects. Is that the case?
And also just to clarify: You describe what happens as being a "loophole in the system" - Does that mean that itch does not permit developers to remove files in this way, and for the times that it does happen, itch at least has the authority (if not the capability) to undo the changes?