We prevent creators from removing projects. We don't prevent them from removing files. That's the loophole. And we don't keep backups of those files, to the best of my knowledge (I could be wrong). So we can't undo the changes ourselves either. How would we even be sure when it's justified to do it? Most creators change files in order to give players new versions of a game, which is a good thing and shouldn't be made difficult.
If itch does not keep backups of anything, then that obviously makes any potential remedy pretty meaningless. I don't know what the financial situation of itch is right now, but if the ability to have at least a single backup is achievable then that's the first step I hope you would make.
As far as changing the rules for developers goes, I think at least one change to the rules could be made stating that developers are not allowed to remove content to such an extreme that it leaves customers who purchased it with virtually nothing - an empty text file as is what happened with my purchase (that has since resolved by the developer), or replacing a game with an image, audio or video file, etc. I can remember at least one instance of Valve reversing a similar change that was done to a game on Steam, so I expect that would be not be a difficult rule to enforce.