@Shelley319 You could set up a third unit that represents the entire duplex, and make your existing units children of that unit. That way, you could book the entire duplex as one unit, but if either of the child units books separately, the dates will correctly show as unavailable on the parent unit. Conversely, if someone rents the whole duplex, the dates will correctly show as unavailable on the individual units.
This strategy also works for whole house vs. individual rooms.