I think the windows may be painted on, that would be the easiest way to only animate translation without anything poking through the windows the layer underneath. All the buildings look like simple animations of translate/scale with a little bounce.
Alternatively, you could use blend shapes: one totally flattened (sans roof) into the full shape, giving that "pulled up" effect.
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Alternatively, you could use blend shapes: one totally flattened (sans roof) into the full shape, giving that "pulled up" effect.