You have a few options.
You can demolish the whole roof and then recreate the piece you want to keep. Once done, you can select that piece and place it in the same phase as the original roof.
Rather than demolishing the roof, you can use the Opening tool found under the modelling tab, and cut away the portion you want to demolish. This method will allow the roof to show correctly in each phase, without the double roof that you get with the first method.