this doesn't seem to be a situation that Turbotax can handle automatically. if I'm wrong I'm sure someone will correct me. the way i would handle it is to manually allocate 1/3 of the interest and taxes to the rental then for the 1098 enter 2/3 of every amount.
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as i understand the rules let's say the mortgage is $1.5 million. there is no mortgage limit for rental so $500K would go there and on the 1098 entries you would report $1 million as the home debt and 2/3 of the interest and taxes (if taxes are on the 1098) .