Try select all then ctrl shift. Instead of selecting the windows you could deselect the six walls, floor, and altar. Tedious, but not as many steps.

But if you actually used an image texture for the windows you can change in the material lab and they all will change.You don't have to select them all. Just pick one and pick the original square in the materials lab instead o fa blank one. Load the new texture and every object that uses that texture will match.