Did you found a answer or got this “fixed”? I have the same problem, I have a structure with two floors, both floors have a valid navmesh. But when a location on the 2nd floor is picked and AI does a AI move to, AI will go to the exactly same spot in x-y coordinates, but to the spot in the lower floor. So it seems AI move to is not understanding Z axis when there are nav meshes vertically stacked for floors.
As I read, after “updating you” nav mesh everything was fine? Or did you also changed your nav mesh to only have one floor again?