Great, an admin response! (Checks user page ... "Hello, I created itch.io." :D I feel honored!)
On point 1: Yes, I mean the analytics only I see, and I'm concerned about the completely wrong situation that I am deriving when looking at the numbers. I only just discovered this (what I would call a) bug, so I can basically throw out most thoughts I had constructed in the last week regarding my downloads :/
If one has high download numbers, the small changes caused by one's own downloads wouldn't really matter, but there are enough beginners that will have their numbers unpleasantly and confusingly skewed by this, and I don't see why those downloads are counted in the first place: itch.io's code certainly knows for every action taken whether a user is logged in, so why not just prevent counting if someone downloads their own stuff?
2. I wouldn't have deleted but just set invisible the file, because for a few versions this is certainly ok and doesn't get too cluttered - but I don't see why the clutter is necessary at all. Can't the file download history just have entries for deleted files, too (optionally hidden)? You could implement it server-side by having two delete-stages. If you ask yourself, you know that this would benefit users, it would just be yet some more stuff for the to-do list.
Butler might be a workaround, but the term "workaround" says it already, also I haven't read up on it enough yet to know if it would allow to change the uploaded file name while preserving the statistics (if that's in the docs at all ...). Don't see me as spoiled with luxury - I'm just voicing what thousands of content submitters potentially experience when they look at those numbers, miss the old ones, but just move on with other itch.io stuff because they can cope.
3. While we're at it: There's a weird bug in itch.io's text edit panes (e.g. right here, or on tool (or game?) edit page). When I delete text with backspace, the cursor sometimes ends up at position 0 of the whole text. And sometimes, it seems as if the focus is taken away, but maybe that's just pos 0 when the text is longer and I just don't see it any more, not sure. I can't for the life of me reproduce the bug reliably. It seems oddly coincidental. Maybe it's timing-related and also only occurs when the browser has a bit more calculation load. (Using Firefox on two Win 10 computers, both are affected, never had this on any other site.)
4. Another thing I just remembered. I recently tested the itch.io desktop app, which makes a quite solid impression. What I didn't like though was that it changed the name of the file I downloaded: I used it on my own submission, and the downloaded file had a different name than the original. This interferes with the applications functionality, since it drops a launcher&updater which in turn works by analyzing the file names to determine the newest version. I don't see why not the original name is used. It's a file name, after all, there's not much room for exploits. If anything, only automatically change filenames that use right-to-left special characters and such.