You might try asking around in your area the reason for doing this. I have lived in several homes of that age in Pa. and seen many more around here and haven’t seen this done. Did the person doing the energy audit have any suggestions on what others have done with this condition or why they did it back in the day? Is new construction still filling the areas? Does your wood show any signs of rot where it is next to the fill? I guess you will have to just pick a place and remove the fill in one bay and see what you find and also get an idea how hard it will be to remove. I personally don’t see where it is doing anything.