If a card tells you to swap the placement of two rooms in any dungeon and you have multiple rooms on top of each other do you swap the placement of just the room on top of the stack or do you move the whole stack of rooms?
For the purposes of moving rooms, a room is made up of every card in the stack at each of the five positions in your dungeon.
So when a card tells you to move a room, you move every card in that stack.
From the FAQs & Advanced Rules section of the rulebook (page 19):
When an effect allows you to swap the placement of Rooms in a dungeon, how do you deal with Rooms built on top of other Rooms?
You can rearrange any stacks of Rooms, but you cannot change the order of Rooms within each stack. The visible Rooms do not change.