If I'm not mistaken, the windows you referred to were intact.
Don't mistake my comment, I don't object to them staying with the building.
One of the main panels (center window) is gone, and would be impossable to replace in order to match the theme of the window.
As to the bottom panels that are gone, since they are simply stained glass minus art work, they could be replaced easier.
The windows are about 100 years old and need to be looked over by experts anyway and where needed re-leaded in order to preserve them.