I'm also tweaking the Okeno section but i a different direction. I saw someone had used a colour out of space and decided to give it a go.
There are 88 creatures in Blossoming Thorn, and a total of 778 Charisma available. The Colour's Aura of Lassitude prevents prey from leaving and only Biting Lash has a decent Will save. Assuming some occasional great rolls cause a sentient creature to wise up and flee, there's plenty of food for the colour to grow 5-7 HD. 6 HD makes it a CR 14 encounter, on par with the Keeper.
My timeline is >
Lowls enters the Soul of the Mysterium.
Under Weirelai's (I bumped up her role so she was the captain of the Bloodwind and is guiding Lowls. HIs first attempt at contact an entity got him Weirelai) suggestion, Lowls studies the Necronomicon while the Denizen of Leng makes for Okeno. The Keeper gets corrupted by Xhamen Dor while keeping tabs on Lowls' thoughts.
Lowls mastered the index and then mastered the teleportation section (Again Weirelai advised him on what to do). The Corrupted Keeper let's Lowls escape, THEN triggers the now corrupted wards itself to trap any who would follow.
Lowls, now in Okeno, meets with Weirelai and they talk to Biting Lash to get their expedition together. Weirelai pays Biting Lash in a pile of Leng rubies and a halfling sized ruby that that shimmers with inner light. The denizen explains that the extra large stone is payment for their silence. Actually, it's a meteorite containing a Colour. They set off the next day.
A week later, the PCs enter the Mysterium and mind shattering hilarity ensues for a couple of days. They slay the Corrupted Keeper and it reincarnates as a Lantern Archon for it's failure. The shamed archon tells the PCs what has occurred, and also tells them something it gleaned from Lowls' mind - the passphrase to safely open the Necronomicon. "Geir et necriles hyades" (the creator, the tongue, and the origin).
In Okeno, right around the time that Lowls and crew set off on their expedition, the Colour-ful ruby cracks open. Over the course of the next week it feeds and drains on the gnolls, then the animals and beasts, then the slaves.
Kisetz and Hakoor are bruisers only with no prior connection to the PCs. They slip away immediately to tip off Biting Lash for a reward, and are either killed or fed on by the Colour.
I will be running the Blossoming Thorn section with players seeing the aftermath and desperation of gnolls trying to flee the Colour or simply lying down to die (most colonies in the Aliens franchise, zombie apocalypse movies, Planet Miranda, etc). A majority of the living things in the fortress are either colour-blighted or reduced to yet another pile of drifting powdery ash.
Kaklatath's high Will saves are keeping her safe, but she's trapped in her cell.