Personal experience with this...
I used to live on the Colorado river in north-west Arizona (USA). The US Army occasionally flies terrain-following heli missions down the river (the river is about 100m wide and has 8-10m banks at this point - nicely hides helicopters visually and acoustically). The helis (usually Apaches or Blackhawks) would pass the back of my house at a distance of about 75m and roughly on the same level. While I never sustained any damage from the rotor tip shock wave, the plate glass windows along the back of the house rattled enough to bring me running. Had they been closer than 50m, there is a good chance that there would have been some damage to the windows. The sound of the shock wave hitting the glass (at under 100m) was like that of a towel-wrapped stone lobbed at the glass - a nice solid BANG! each time.
Also, these were not some custom-fitted glass, but standard patio sliding panels - about 2m tall and 1m wide, mounted in aluminum frames with rubber gaskets holding the glass. Had these been "hard" mounted (ie, hardened glazing putty in a rigid metal frame), it might have been possible to cause breakage.
So, if the MoD *DID* do the damage, just how close and at what attitude would the helicopter have to be in order to cause it? Unless the helicopter was flying at near ground level and 50m or less away, and for more than a few seconds, I would certainly be having a stern discussion with the builder and the architect.
Just me nickel's worth...I'll get the coat now...