The original impression I got was that Klute had been looking for Czevak ever since Czevak was taken to the Black Library from the crashed craftworld digsite in the opening chapter. However, the interregna chapter where Czevak is on the battle cruiser
Indomitable and subsequently captured by Ahriman shows that Czevak was actually back with Klute and the Imperium after his first stay in the Black Library. So... Czevak spent some time in the Library, then got back to the Imperium... how? Was it only
after Ahriman captured him that Klute began his search for Czevak?
As far as I can piece it together, this is what I believe the order of general events to be:
- Czevak is taken to the Black Library from the crashed craftworld digsite
- got back to the Imperium somehow - after enough time that Klute was now an inquisitor himself

- captured by Ahriman (how did Ahriman get hold of Joaqhuine? Was she even real, or just another warp-trick?)
- Klute begins (resumes?) his search for Czevak
- Czevak is rescued from Ahriman's ship by the Harlequins
- imprisoned in the Black Library
- Ahriman got into the Webway?
- Czevak escaped with the Atlas Infernal with Adara-Ke's help
- roamed the webway for an indeterminate amount of time, de-ageing and learning how to use the Atlas Infernal
- emerged on the rogue trader ship from the portal that Klute had found during his searches
- various adventures with Klute and the others aboard the rogue trader
- Czevak goes to Melmoth's world, flips off Ahriman, and kills the tzeentch daemon Mammoshad
- rogue trader ship is pursued by Ahriman's fleet (apparently there because Ahriman from ~50 years ago warned himself in the future, or something?), escapes through a webway portal and into a webway drydock
- Czevak basically tells the Harlequins that have been pursuing him to get lost and melts the shadowseer with the Atlas Infernal
- they ride off into the sunse-- er, Eye of Terror, with the implied intention of giving Ahriman many Very Bad Days.
Is that about right?
And! It's mentioned that Ahriman managed to get into the webway through information he'd taken from Czevak (I didn't quite get if he'd actually made it into the Library or not - all it mentioned was "sacred thresholds", though I'm assuming it was just the webway and not the Library itself) and was having more success than the Eldar had predicted - but it doesn't mention what Ahriman was doing, how the eldar got Ahriman out of the webway, or even if they did.
So. Confused.