Mocha + Mocha Shape should do this nicely. Track large chunks of the building separately, on their individual planes. Within each plane, create X or B Splines to mask out individual lights/windows. Export the shapes individually and paste them in AE, onto a duplicate of your backplate. Change the Shape Colour to a black hue and animate Opacity (with the effect) to bring on the lighted version.
Lots of shapes are required to export but once you’ve tracked a plane, you simply have to link it to the shape layers that cut out the windows. So, track once and you will be able to link the tracked data to any new shape within the same plane.
HTH
RoRK
AE Training in South East Asia. AE templates for sale and rental. Click here for more