I’m a little confused about lairs in already settled domains. If you clear a hex does it stay cleared forever? Does it only stay clear if the hex is civilized? If it does repopulate lairs how do you figure out when they repopulate? If they don’t repopulate and you roll a lair encounter in a cleared hex does it default to just a regular wilderness encounter?
They can repopulate, but the frequency of checks for whether a monster passes through the area (and could potentially decide to stay) is reduced as the area becomes more civilized and the odds of whether a check produces a monster may also fall.
Note that these factors also apply to wandering monster checks when PCs are traveling - a mountain hex has a 4+ (on 1d6) chance of an encounter each time they enter the hex while its wilderness, but, if a dwarven vault is built there and grows to the point of it being a civilized domain, the encounter chance drops to 6+ and is only rolled once a month, no matter how many times the PCs enter or leave. So, even if any individual encounter may still have the same “in lair” chance, encounters will happen far less often in settled domains.
Plus, of course, the domain’s garrison is likely to repel any lesser monsters who get ideas about moving into settled lands, so any monsters that do attempt to repopulate lairs may not be staying for long.
 Populating a Dungeon, ACKS 141-142
 Encounter Frequency by Terrain table, ACKS 244
nDervish said: Plus, of course, the domain’s garrison is likely to repel any lesser monsters who get ideas about moving into settled lands, so any monsters that do attempt to repopulate lairs may not be staying for long.
I always assumed that this is primarily what the lower frequency of rolls represents
That too, yes. But, when I posted that, I was thinking more along the lines of after the once-a-month roll turns up some kobolds and the kobolds have decided to build a lair just outside the city, they’re more likely to be driven out by the city’s garrison rather than staying there until the PCs do something about it. (Unless the city guards hire the PCs to do something about the kobolds for them, of course!)
I would interpret it to mean that the number of lairs might not necessarily change, but the type of lairs would. So, instead of primarily ogres and kobolds and dragons and stuff, the adventurers now have to deal with a cabal of evil cultists converting the local peasants, a doppelganger infiltrating the City Council, ghouls in the sewers, etc. Also, you could treat the presence of some lairs not as containing actual monsters, but rather obstacles. As a domain becomes more civilized you’ve got to worry less about orc raids and more about outbreaks of cholera, for example.