Page 88 of the Hardcover states, that the Direption was visiting the city several times over the course of the years 4703–4711, but that at some point after that the ship was reported as “lost” by its owner.
On page 37 of ISWG under the year 4708 we can read that an aging King Eodred retreats from rule of Korvosa, leaving his untested young wife, Queen Ileosa, in charge of Varisia’s largest city.
I always thought, according to canon, this AP would play out in 4708. Is this just a minor error, or did I get something wrong?
I don't believe that there is an actually official year for this play out. I think you can run it whenever you want too. It is whatever suits your campaign timeline. I am playing my in 4017.
That being said, according to the ISWG the current year is 4011. Eodred is still alive and only retreated from rule at this point. Given that, it makes sense that in 4011 the Direption is lost and Eodred is murdered by Ileosa.
I think the timelines changed when they did the switch from 3.5 to Pathfinder RPG. I could be wrong though.
Funny enough, I had this same issue - they did update the timeline for the hardcover release. If you're adjusting the year, then you need to account for this. I believe the current year in the hardcover is 4716, which means that the Direption last visited Korvosa five years ago. Since I'm running the AP in 4708 also, that means it could not have visited more recently than 4703. Somewhere in there, the ship goes missing.
In short - yes, there's a disconnect in the years, so you'll need to adjust the info accordingly.