When playing a new tech adept, owning both Warhammer 40k Inquisitor: Prophecy and Martyr, if you launch from Martyr you cannot progress past the 2nd chapter 1 mission 

Repro Steps
Create and Play a new Tech-adept in warhammer 40k inquisitor martyr launchable.

Beat the first two Chapter one missions

Cannot progress past the 2nd mission

Work around is to play the Tech Adept in the Prophecy Standalone exe