Yes, you can still claim it as a rental while it was undergoing repairs, if your intent was for the property to remain a rental. You would claim the repairs the same way you claim other expenses for a rental, as repairs and maintenance. Since the repairs took more than a year, it raises the question of whether some, or all of the expenditures for "repairs" are improvements, or repair and maintenance expenses. If improvements, they need to be capitalized and depreciated.
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You will enter them as rental expenses on Schedule E. When you walk through the rental income and expenses section, just leave rental income blank and then continue through to enter your rental expenses and improvements.
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