Actually I think this bit of plot is one that we should universally agree not to discuss...Because well, Corypheus is both powerful and essentially immortal, and he has a bloody superpowered dragon. And Samson is apparently invincible as well. So why not just kick down Skyhold's door himself? It's not like the early Skyhold inquisition has the ability to fend off even a normal high dragon, let alone the red lyrium one....And it's not like the inquisition is hidden in covert cells. Unless Skyhold has evil-proof shielding, I can't see a reason why Corypheus doesn't do that.
It's such a game-breaking plot hole that I can't bear to delve further.
It can't? Says who?
The day after the Inquisition finds Skyhold, sure, too weak to stand. By the time Corypheus knows that the Inquisition has survived, pinpoints Skyhold and gets troops in position to attack? By then months would have passed, and Skyhold would be strong enough to either hold them off or cost Corypheus a very very great deal.
This is all assuming Corypheus has any real intention of attacking the Inquisition, which he does not. He attacked Haven for two reasons. First, he was angry that the Inquisition got one of his armies. He suffered a loss and had to answer. But more importantly, he attacked Haven to get the Mark off the Herald. Something he concluded it was impossible to do. With his power demonstrated by destroying Haven and the anchor unrecoverable, he has no need to go toe to toe with the Inquisition. He certainly has no reason to suspect that they are a threat.
Let's not forget that the only reason the Inquisition is a threat to Corypheus is because they know exactly what he is going to do. Either the Inquisitor saw the future or the Inquisitor met someone who spent weeks/months hanging out with Corypheus' forces while capable of mind reading. Whichever it is, the Inquisition knows exactly what Corypheus has planned and is able to insert themselves into everything he is up to.
If not for knowledge the Inquisition had no reasonable way to have obtained, by the time they figured out their next move it would have been too late to stop Corypheus' plans. Orlais would have fallen and Corypheus would have a demon army. Game over.
So Corypheus would, at best, have to devote significant resources to destroying Skyhold all for no real strategic gain. At worst, he would spent almost everything he has directly confronting an enemy he has no reason to fight.