Existing Building undergoing major renovation

I think you need to apply some sense of logic to these situations. As an example, would it be appropriate to model an existing condition as an open hole in the wall even if that was the case? Assuming that the current opening will be filled with windows I would model windows in the baseline. If this is an old building that had windows, I would likely model single pane windows in the baseline, not plywood. If this was a newer building, say built since the common use of double pane glass, I would use a double pane window. If the building had metal frames, I would use that in the baseline. If wood frames, I would use that. There are values in Table A8.2 for unlabeled vertical fenestration you could use as a default.

Sounds right and with a SHGC entered for the windows your baseline will be a more thermodynamically comparable model to the Proposed.