I think it does an as-needed HD diagnostic sometime during the update process, so it may not go through the whole thing every night. I only had it happen once on its own, I deleted a few month old recording and it just kind of sat there confused and all of a sudden the HD diagnostic kicked in. As I recall, it was supposed to run for about 45 minutes, according to the info on the screen. Luckily it was around 11 pm so I just let it finish overnight. The next morning all appeared ok, but the show I tried to delete was still there, but then I was able to delete it without a problem.