Very good analysis. One thing: the BBEGs have intelligence as to the state of the attackers. The escape lieutenant very specifically observed until his force was overwhelmed and then escaped. He knows how beat down the party is and that they lost their healer. He doesn't know what decisions the party made after he left, but as beings that exist in the world, they can make some guesses. If the PCs don't push immediately through the portal (he can guess they know where he went) then they can surmise they are too worn to try right then. But if they haven't broken the link, they can surmise the party plans to use the portal. Either they are going to flee the fortress and escape, or perhaps rest and then return, scouting themselves or possibly coming in with overwhelming force (the party could be the vanguard of a larger force, after all).
The lieutenant is going to say "I ran away from a nearly defeated force"?
Or "they where overwealming and I did all I could to stop them?"
Mechanically... the lieutenant doesn't know if the PCs have sending, and now that they have found the permanent teleportation circle in the citadel will summon massive reinforcements via teleportation circle.
Second, you may notice that the 5e MM monsters rarely have abilities that line up with PC class abilities. By default in 5e,
PC rules do not reflect how creatures work. You can choose to make this the case, but this is a choice. (And if you take that to a logical extreme, you get a gonzo world; most people who do it do it extremely selectively).
The PCs, if not dumb, are going to set up traps at the teleportation circle. (The PCs apparently are dumb, but the NPCs shouldn't assume that). The initial attack should be sacrificial, or even an invisible familiar peeking.
So, to me as DM, it makes sense that the duergar will send a scouting force back into their outpost after a couple of hours
A couple of hours makes no sense to me. (I suppose if your creatures in the world have an exact knowledge that resting between 1 and 8 hours generates next to no benefit, but that is a very gonzo model of game reality to me.)
A couple of hours means that if the enemy has nearby reinforcements, they'll be there. It gives them time to fortify the teleportation circle. It means if they are at the teleportation circle, they think they can defeat anything that comes through. You completely gave up tempo of the fight.
Either you do it right away (as soon as possible) to attack the enemy while they have no time to prepare, or you basically don't do it at all.
Think WW2. Your front lines are overrun. You fall back. You counter attack the moment you can muster enough forces; you don't give the enemy any longer a break to fortify or recover than you can.
-- not long enough for the invaders to get fully rested or muster a very large force, but after enough time that the scouts should be able to ascertain what the plan is. If the scouts don't return, the BBEG will likely just break the link -- there is just too much uncertainty about what is happening. But potentially, the scouts can finish off the interlopers and bring back one or two for questioning to find out what the Council of Speakers knows about the duergars' plans.
A force large enough to defeat (even the wounded PCs) isn't a
scouting force. These beings are damaged and exhausted, but they still completely overran a fortified and defended location that guarded a back-door logistical pathway to the "core" of your army.
I mean, if a
scouting force could be enough to defeat the (wounded) PCs, why was the fort so lightly defended in the first place? Add on a mere scouting force, and this strategic location would have held, and the PCs would have been defeated. Either the defenders are strategic idiots (possible), or their total available force budget was seriously impacted by the PCs attack.
It is a full on counter attack. They have to account for being in a worse position, strategically and tactically -- a bottleneck, no fortifications, exactly where the defenders most expect an attack to come from.
I mean, even if the fort was an undermanned sacrificial position, then the counter-attack should have been ready to go and gone through the portal
before the PCs overran the fort, so that the teleportation circle wasn't in risk of being destroyed by a tiny enemy attack.
I just don't get the strategic plan of your NPCs. You don't guard exposed yet valuable logistical bottlenecks with a token force. And if it wasn't token, then mustering forces from the main base to retake it should be a significantly large part of their forces, which means that sacrificing those forces should be both a huge expense and risk.
In short:
You can justify anything you want to justify with "DM my guy" syndrome, by selectively picking what parts you consider "well, that only makes sense, I guess I have to do X".
Here, to me, it appears you want the choice of "take a long rest" to be a bad decision, while "advance" or "take a short rest" or "destroy circle" would be a good decision. So the enemy tactics happen to line up with "take a long rest" being the worst decision.
Not only from what the PCs experienced, but from abstract strategic considerations implied by a fort with a teleportation circle leading to access to a main base, I could make a reasonable justification for any of those being the worst decision and any of them being the best decision to make.
So feel free to make the PCs decision be a bad one. It really is up to you.