not sure if it's the same in AE but in Project Dogwaffle's DoggyFX plugin there's animated masks and I guess in other apps too, when you want to blend a video frame for frame into another in a particular area you can use a mask. It's like an alpha channel that selectes the pixels which are eligible to receive the second video to be blended into or over the first. The mask is however not just a do or don't thing, it's not necessarily tied to being a full selection or full de-selection of the pixels. It is a weight factor (8-bit alpha value) that can indicate the percentage of blending to apply. If the value is 0 (zero) no effect occurs. If it's 255 (100%) the full blow of the incoming video is applied over the existing video. Anything in-between, and you get a partial, subdue'd effect.

You can then use an animated mask, i.e. one that changes over time. PErhaps it changes in selection topology (shape), perhaps it changes in the intensity of the selection, perhaps it changes both. At any rate, you can 'fade away' the amount of the mask letting the explosion effect in, and thus make something disappear. For example, if you do have the same scene 'without the building' (is it layered?) you can gradually superimpose the scene without the building over the pre-existing scene with the building. Gradually, or suddenly - just before the smoke lifts.