Strange things happened to me as well.
- I defeated Fort Deadlight early on, but spared Benweth's life.
- Then I got the missive from Aeldys, but didn't pay her a visit.
- Then I cleared up Magran's Teeth, and the first time I've personally seen Aeldys was when she barged in at the debriefing at the royal palace.
- Then I went to Dunnage (because the Valians wanted me to have a chat with them), met with Furrante, he gave me two questlines: go to Crookspur and talk to their leader, and to hunt down the ghost ship. After I left Dunnage, I immediately got two missives: one from Furrante, telling me where to go for the ghost ship (strangely, it doesn't appear as a quest, the "Symbols of Death" is closed after I gave the info about the undead paladin), and one from Aeldys, who wrote she regrets I didn't pay her a visit the first time she invited me (so the devs had taken that into account!).
- So I went to Deadlight to meet Aeldys, I even prepared her favorite candy, but she is nowhere to be found! In the Command room, there are desks with maps, she's not there. There is a side room with the fireplace with many discarded nutshells, so I assume it's her room, because candied nuts are her favorite. But she's not there either. I never ever set foot on Crookspur yet, so those quests should not have been progressed.
Did I miss something, or is it a bug?
(Edit: I've read Furrante's missive again, and I realized he organized a meeting first before going for the ghost ship... so I went back to Dunnage, and I found out why Aeldys wasn't at her base: she was tied up at that meeting. I still keep this information for any others who happen to get baffled by this same order of events)