All three of them actually have about as solid a timeline as you can get in 40K. The Eisenhorn books and their related series are set from the early 200s to the late 400s of the 41st Millennium, so he's either dead or incredibly old at the current point in the timeline. The Gaunt's Ghosts series takes place during the Sabbat Worlds Crusade, which ran from the mid to late 700s.M41 and possibly into the early 800s (Abnett hasn't finished the series, so who knows how long it'll last), so again Gaunt is either really old or really dead by the Indomitus Crusade. Cain was active from the early 900s.M41 all the way up to the 13th Black Crusade and then is said to have died at some unspecified point in M42, after which Amberley started editing and releasing his memoirs, which he'd started working on a few years prior to the Black Crusade. None of that has been affected by the retcon, as far as I know, even with the line in the first Dark Imperium book where Guilliman is musing about how absolutely fucked the Imperial calendar is. Tbh, I'd like a Cain novel set during the Indomitus Crusade just to see how he'd react to stuff like the Great Rift and Guilliman's return.