First and foremost, thank all of you for bearing with me as I'm taking baby steps forward and (quite large) strides backwards. Luckily the latter occurs far less than the former
Zoeyk alerted me last week that the game database was missing games. After my initial panic I saw that indeed there were no games in there starting from late 2006 all the way until late August 28th. I am still unsure how that happened. Luckily, we had a backup of the database when we moved the website, but there was a week of games that were not backed up. This weekend we moved the missing moves back into the database. To put some numbers on it, it's about 13-14 million rows (moves) that had to be inserted in a database of 6 million rows and make sure that we avoided duplication. This operation, to my surprise, took almost 20 hours.
As far as I can see, all games are back except that week. I had hoped this would have fixed the issue with the turn-based ratings graph, but alas, that requires some more time and digging.