On the download history page there are two buttons. One "mark all as updated" and one "remove eveything". I misunderstood the second of these to mean "remove everything on this page" whereas actually (according to the tool tip I noticed afterwards) it clears your entire download history. Why wouldn't it? Dohhh!
Now this was my own silly fault, I accept, but it would be good to have a "Are you really, really, sure you want to forget about all these add-ons that are being constantly updated, hmmm?" button.