Select the building. Polygon level, select the single poly which has the problem - that's the whole side with the windows in it (Polygon 319). Detach to a new object.
Select the new object (Object082 if you didn't change its name), Right-click > Hide Unselected. Border level, carefully select all of the borders around each window. I would Ctrl+click them one at a time to make certain you don't pick a "bad" edge.
Extrude (small button next to the Extrude button to get the Caddy). Default of 10mm is fine, but zero out the width. Note - it took my system quite a noticable time to do the extrusion - no doubt because of the problems within the object (that non-removable "poly"). OK the Caddy.
Deselect the object. With 3D Snaps to Vertices, create a new Plane object, 1 segment in both directions, to cover the entire object (snap to diagonally opposite corners of the original). Turn on Relative transforms and move the new Plane 5mm so it intersects with the extruded openings on the other object.
ProBoolean, Subtract and Cookie, then pick the old (extruded) object. You should get a nice, clean version of what was there before. Convert it to Editable Poly, Move it back into position (-5mm).
Right-click > Unhide All. Select the main building > Attach > pick the new object. Right-click > Object Properties > Backface Cull. Make sure the newly attached side is facing the right way (outwards) - if not, select it (polygon) and Flip it. Vertex level, area-select around where the vertices of the new object and the building meet (Left viewport would be best for this) then Weld them.
As you found to your cost, playing fast and loose with booleans is not always the best idea. Use them sparingly, only in situations which have no simple alternative, and you should be OK.
One final point - a building that size is unlikely to be 535 by 352 mm. Unless you have a very good reason for building it at that size, you really should create models at their real world size. Many things in Max such as certain Materials, physics simulations etc all depend on objects being the correct, real, dimensions.
Max 2016 (SP1/EXT1)
Win7Pro x64 (SP1). i5-3570K @ 4.4GHz, 8Gb Ram, DX11.
nVidia GTX760 (2GB) (Driver 430.86).