Que pasa?
 

I saw the global message Stefan sent about restarting the servers, and then a few minutes later all of the npcs in the control dissapeared except the ones that I was working on.
Does anyone know what might have happened?

all stefan did was restart the servers so that he could fix a connection problem and i think disable v2.2. He never deleted any npcs so it mustve been that right before he restarted your server you mustve been doing/working on something therefore the data was lost, or you probably made a mistake which caused that to happen. Unless stefan clicked the wrong button XD (lol).

All files should still be there.
Are they back yet? (Try restarting NPC Server)
If not forumPM for a backup restore.