I run a website which has been active for well over a year (www.yogscast.cookingwithhannah.com) and last time I checked it had roughly 33,000 comments on it (many through the use of Genki's Youtube comment plugin, which although being out of date has been working fine consistently).
It was fine yesterday, came back today and no comments exist anywhere on the site. The dashboard doesn't remember having had any, although Akismet tells me it has protected the site from 1,273 spam comments already since July of this year - it can't find any of those either. There are roughly 2,500 entries in the comments section of the SQL database which it can't recognise either that I am guessing are only a small portion of the missing comments.
I've tried disabling all plugins - no joy. I've tried slowly adding them one by one - no joy. Nothing on the site has changed at all. I've even tried making a new post and going through the usual procedure. The addon tells me it has added 25 new comments to the latest post, lists each of them as usual, but when I go to the actual website, nothing is there.