So I logged off after doing the Purst Pig Farm quest and logged in a couple hours later after the server had reset only to find that all the loot I had obtained from the quest had disappeared.

Server roll-back. It crashed almost immediately after we finished. It happens, and it's something that can't really be fixed except by making the server backup the character files more often - which probably isn't very feasible.

Character files should be saved on logout, so I'm not sure what happened here.