Have you set the linked file to be Room Bounding? If not, do so by selecting the link in your host file and, in the Properties palette, select the Edit Type tool (just under the Type Selector, at the top). In the Type Properties dialog, find the Room Bounding property under the Constraints category and select the toggle in the Value column to put a check mark in the box.
If, as you describe, your rooms were taking the shape of the previous layout rooms, you may need to do some work in the host file, to either delete the Walls in the renovation area that are no longer present or set up Phasing and demolish those Walls.
David Koch
AutoCAD Architecture and Revit User
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