It depends. If you are selling the property, you will need to use Form 4797, Sale of Business Property and Involuntary Conversions of Assets. If you are not selling, you will follow the interview questions to access the "asset"" (the roof) and "sell" it for $0. That will put your remaining basis below $0 which effectively "uses up" the remaining depreciation.
Here is a TurboTax article about managing assets.
