Basically I went from having 90K to 1K and I know that I haven't spent it. Unless thieves are capable of stealing in mass quantity then I probably ran into a bug. Is this something that's come up before? I'm familiar with the additem command but how safe is it?
Just open the console and type "additem F 89000" with your character as the reference. It's completely safe as I've been using it to award my character with self made quests for 90 ingame days so far. Works like a charm.