Nice to hear that you already are considering in changing it :) It would be nice if you could look up the numbers of the two replaced/deleted numbers but only if it isn't a lot of work. I have the numbers from a day before and wrote the complete download numbers down after it happened and can calculate them with a margin of error which is definitely enough for the postmortem.
Does it affect the ranking when I delete a file? I think many developers would consider deleting their "Hidden Files" (and free up storage) if they would keep the statistics and would know if it affects the ranking.