As I look at what's transpired in Stonehell, the release of Ka-Nefar is probably the biggest change. Everything else has been merely a cleaning out of the dungeon. Ka-Nefar adds something to it. As he solidifies his hold on upper levels of Stonehell, the nexus feeds his power in the guise of the Black Sun. This allows the dungeon to restock, and fill with harder things than otherwise might initially appear. But the changes are all tied to Ka-Nefar. If he is defeated, the influence of the Black Sun will wane.
Level 1 - Lots of insect swarms and giant insects - 2/6 chance for random encounters
Quiet Halls Lots of lesser undead. LOTS! Mal is now a mummy lord
Contested, and Kobold Korners each commanded by a mummy lord.
Antechamber isn't bothered with much, but the Zunbar the Troll has moved in and has attracted a tribe of goblins who've been eating troll flesh. Chosen of Zunbar.
Level 2 - 2/6 chance for random encounters
Asylum - proliferation of ghosts, shadows and other non/semi-corporeal monsters.
Reptile House - Lizardmen wights, lots of roving lesser undead.
Without Doors - ghosts, Hobgoblins Ghouls, & Slimes
Hobgoblin - Hobgoblin Ghouls & Wights
Dorm - Rats are super upset, undead moving in. Harpies are feeling the squeeze, move back into shaft as gargoyle tribe cut down.
Hex - Fulkith hired gobgoblins and bugbears. The bugbears have been paid to work for the party, hobgoblins figured it out.
With the upper levels solidified, Ka-Nefar is bringing the fight to the vampire lord, and has destroyed his back up coffin, and is expanding into that level. Last of the Mummy Lords is heading up that fight.
Rocky has several old messages for Eiric from Sniv. Misses everyone's visits. The goblins are very talkative, so that keeps him from being lonely.
Sniv has moved whole tribe to the caves, getting ready to leave the area.
Zunbar isn't really with it, but likes how the goblins bring him things, spends lots of time in the water.
Wererats have rats posted all over to keep an eye on the party. Want Undead dealt with. Thinking about heading deeper to get away from them, but out of treasure.
Lachkis thinks the party might be useful
Fulkith (Wiz 9) warned by hobgoblins of bugbear treachery, Bugbear chief maims takes all the gold. Rest of the bugbears mad about losing the extra pay. Will revolt if given the chance.
What's next? I don't know...