I did something similiar several years ago for a mockup demo of cyberpunk-themed "Jagged Alliance" clone which was supposed to have large maps filled with skyscrapers. It was a stupid idea, apparently maps for tactical combat should be tidy and easily understandable :)
In order to have a quicker pathfinding one global map was divided into several discrete square-shaped areas. Once we have a criteria for areas, it's time to find possible "entrances" between each pair of adjacent areas. "Entrance" is a transition point which shows that this agent can enter this area at this point.
In your example with building of several floors, each floor would be an area with borders defined by floor, ceiling and outer walls; and varius holes in wall or floor, or ladders would be entrances, there could be a lot of them. So entrances basically link path nodes from one area to path nodes in the other area.
Once you identified entrances, you'll need to find all possible ways to traverse each area resulting in a "map of area entrances to adjacent area entrances" with edges between entrances showing length of this path through area.
If everything went right, your agent standing on the 1-st floor will be able to find its way to that special box on the 4-th floor quickly. Maybe something similiar could be used in your problem of multiple maps, so hope it helps.