I never encountered such as situation so I try to say what I would do.
I would set the stories as in the "new" status and draw the existing parts accordingly. You will need more the new story than the existing.
Or alternatively I would use two models ... At the end it seems that you have to demolish almost totally the house ... So what's the benefit to have both statuses in one model?
Hope it helps.
eng. Alessandro Mandala - Italy
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