I'd probably have a project file for each building and one (3D only) site plan file for elevations and renders where I hotlink both buildings story by story and adjust those in 3D as needed to get them right.
Stitch together the floorplan by placing the saved views together. You can export them as PMK file for quick updating and linking.
I would reconsider which story belongs to which since you will need to show stairs or ramps connecting them and that might get confusing otherwise.
For what it's worth, one of the locations of my old university had one such combined set of buildings and people always got lost since 2nd floor of building A connected to 3rd floor of building B etc, so it is not just confusing on paper.
Erwin Edel, Project Lead, Leloup Architectenwww.leloup.nl
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