At times when destructing built structure pieces with the building command it does not refund the resources.
Unless there is a hidden mechanic I don't know about like a grace period before you get no resource refund, the game at times just eats the resources.
I honestly have no clue on what the cause of this might be, maybe lag as for some reason in the morning my connection seems to be rather bad to the server... but you would think with lag it would just drop the resources with a delay, not never...
Resources dropped from destroyed structures will be reabsorbed on contact and applied to other incomplete pieces of the structure. If there aren't any pieces the resource can be applied to, they'll land like normal.
Otherwise, they may have landed out of sight; around a corner, on top of a roof, wherever. Hold E to pick up everything in the area.
If it's neither of these, I don't know what to tell you, sadly.