If you have reported the rental side of the duplex as a separate rental property in the past, you would continue to report it as you have been. For the half that was a personal residence and is now a rental, add it as a new rental property that you converted from personal to rental use.
Yes, you will have two separate properties for Schedule E using the appropriate addresses for each. You will need to manually allocate the shared expenses to each property (TurboTax can't do this for you).
Have you reported the rental on your return at 100% ownership? If you co-own the property and file separate tax returns, you should each report one-half of the income and expenses for both units. But if you are the sole owner, you would report 100% on your return.
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