This refusal is basically because the applicant failed to provide sufficient details of the windows for consideration.
Listed buildings are carefully preserved, and looking at the Heritage Statement prepared by the applicant, the house dates back to the 18th Century and displays a variety of window styles and types (fenestration). This variety very often tell the story of the historic progression of the building which is considered to be important in Historic Buildings.
The documentation refers to some of the windows being Crittall, which are steel and normally single-glazed, and can be cold, draughty and fall into disrepair, but the company still exists and so if these windows are original to that part of the building, then they will be valuable and could be retained/restored. If however they were a later insensitive addition and it can be proven, then there could be a good argument for replacement.
PAPA SAYS - More historic investigation required, identify with mapping and old photographs, prepare a detailed schedule of each window, and large scale sections through the frames for consideration. Not an easy job but then that's why these buildings are listed. Double glazed units are acceptable, but need to be of very slim profile, with glazing bars to match existing to be removed.