The server and games are back up for the time being, as the Windows Server 2012 installation refused to boot because of a BIOS incompatibility. I need to get some new hardware before attempting to upgrade again. May get some tomorrow, but for now I'm uncertain.
When I reloaded the game I realized that we have been running the game without APTMod active since my fuse blew the other day. The icon was hidden away (I am using Stardock Fences to manage my desktop icons), and I specifically remember that I did not start the mod client the last time I reloaded. It is running again now, and I hope this does not cause any issues (If it does, we will need to reload several days backwards in time).