Destroy the entrances and air handling equipment and vents to seal them.
Entrances and air vents are not "destroyed". They are only temporarily damaged. They are merely holes and holes can easily be re-dug.
Then there is the question, "How many entrances are there and how may apparent entrances are decoys?"
Ebensee, Austria Underground Factory Projects "Dachs/Zement"
The only way to permanently neutralized such a complex is to have your infantry in possession of it in order to penetrate it and destroy it completely. Such an airborne operation may have been possible during the Bush Administration but that opportunity passed with Obama in the White House.