That might be a bug with progress not logging properly. This was a huge update and there's some things that may have escaped me. Looking into it.
Edit: I checked this properly and you found a real bug. You aren't missing anything and you do not need to reload your Act I save. The Grave Engine finale was changed to require its final conditions in a single life, but the old 325-year timings were left in place. That makes it impossible with the lifespan you can reasonably have when taking Grave Engine first. I'm fixing it.