It turns out no one deleted them. The problem was that they were written to the wrong directory. The $gameid variable had been set to an empty value in the header, as I was now using $gameid in the header to help find pages for playing games, and I was getting the value from the database. But Game Courier already used this variable without getting it from the database. After changing the header to not set $gameid if it's already set, I located the logs and moved them to the correct directories.
It turns out no one deleted them. The problem was that they were written to the wrong directory. The $gameid variable had been set to an empty value in the header, as I was now using $gameid in the header to help find pages for playing games, and I was getting the value from the database. But Game Courier already used this variable without getting it from the database. After changing the header to not set $gameid if it's already set, I located the logs and moved them to the correct directories.