I just received the answer, and two things, the way the rules are written yes the resources would remain. This is something that was not intended and is set to be cleared up in the first FAQ (I expect it will be delivered some time "shortly" after full release of the game). Upon release of the fact when a questing unit is removed from the quest, all resources will also be removed. Those of you with early releases of the game should probably consider playing this way so as to not have to confuse any newer players to card games and easily mesh with the rules that will be governing the OP program.
Let's hear it for a clean and concise decision that simplifies the rules, delivered in a timely manner!