From a quick glance on the server it appears that everything built in the nether (or at least all the stuff in my general area) has disappeared. Dryturtle also says that he's lost all of the items that he had while he was logged off in the nether. Is this some sort of problem with the coding or was there a reset I wasn't aware of? Did the map size get changed already?

Right. Arth regenned the nether. Same map, but now quartz n shit spawn near spawn as well.