Landmarks question - windows back of the house

i am hoping someone can shed some light on this for me… I submitted my application for new windows in my kitchen for both the side of my house (visible from the street) and the back of the house (not visible from the street). Both windows are the same, matching non-original windows. The one in the back I want to swap out for windows and a door [this is in order to use a mudroom to be converted to a powder room]. This is where I am confused – they said ok to change the windows visible from the street but they think the back window is original and don’t want it changed. They are the same windows, and they approved the change of the one visible from the street (and I have the tax photo from 1940 that shows the original). This is the only option for me to put in a powder room (highly desirable with 2 small kids and no 1st floor bathroom). do I have my architect call them, arrange a site visit, have a hearing? I was told a site visit can uncover work done by the prior owner that may be a violation (such as replacing those original windows). am i opening up a can of worms? What would be the best way to go about this? thanks!