Board Thread:Skyrim/@comment-108.94.85.205-20140622033226/@comment-24261859-20140622042537

You destroyed the brotherhood? As in, you killed Astrid and everyone else? If that's the case, then it never gets "destroyed," just everyone inside dies.

If you join them and complete the questline, the Penitus Oculatus destroys the sanctuary with explosives. It shouldn't be repaired ever.