Treat the duplex as 2 separate units ... a repair on the rental side goes to the Sch E or added as an asset on the Sch E. So replace/repair a window on the rental side it goes to the Sch E. Now paint the entire duplex, or roof the entire building then you need to allocate the cost accordingly. If both sides are the same size then dividing the cost 50/50 would be understandable.
