mmu1,
Perhaps you haven't been reading the thread from the beginning
The PCs want into the fort which is unbeknowst to them taken over by Kobolds. The PCs want to get into the fort, because they are FLEEING from an enemy tribe, and are protecting innocent others. They can't just hide 60 people in the fort while they chase off after the kobolds. They can't hide the others in the Wilderness either. Because then the ENEMY, which is probably interested in wiping out the stragglers, may just come along. Wouldn't the PCs like that?
Now how long they have been in the fort is a matter for conjecture. Given that they have had time to set up defenses, and a tunnel system, the job of the PCs is very difficult
The reason they end up chasing the kobolds is because the Kobolds do not like being evicted, and harry the PCs. Hoping not to win a battle, but hastle the PCs so much they leave.
"Scry, Teleport and Slaughter BBEG" while a beloved tactic of some teams of PCs, doesn't always work. If it always does in your game, fine. I prefer to challenge the PCs, and make them work for their living. You just want High Level PCs to slaughter everything. A simple counter to STSB is the smokey interior. You can’t identify the room clearly enough. Which makes teleporting in a hazardous affair.
BTW, I notice you are using a large number of resources to tackle these "pests", WHICH IS THE POINT!!! The idea isn't "They can slaughter the PCs mwahahahahaha" The idea is "We can cause them to spend so much effort that it isn't really worth their time. IF 400 kobolds CAN'T do this, then their would be NO kobolds alive. SO much for "metagaming" out the wazoo. It would be easier, much easier for these players to create a brand new fort!!
CR13 = 20% of the resources of a 13th level party!
You've mentioned Scry, Teleport, Cloudkill x2, Improved Inivisibility, Darkness (not just on one PC, I assume), Stoneskin (How much did that spell cost again? That is far more than they'll earn on this adventure!), Fly…
Assume 24 Int. A 13th level specialist wizard has: 3 7th, 4 6th, 5 5th level spells per day.
20% of that is 1 7th, 1 5th and 1 5th level spell…
You’d spent 3 5th level spells (Teleport, 2x Cloudkill) A whole bunch of buffs, just to eradicate 400 kobolds? And it can’t be done in a single day? So they are also causing the party to use another precious resource, TIME…
I assume the other players wouldn’t just wander around without their buffs up in a war zone either.
A third thing is; How in the metagaming context of wazoo, do the players KNOW they are only facing kobolds?? The element of the unknown preys on the mind of the players. Clever illusions and mock ups cause the PCs initial concern, and can be used efficiently to sow confusion.
Seems to me like it might just be a CR 13 encounter. Although it is much more difficult to gauge, given the fact that it is a running battle
Finally: If you cannot challenge PCs with this encounter, then you are lacking in imagination.