I uploaded a video of how I beat the AFOS in the chronicle mission. Part 1 is the battle against Nora and Ivanov, part 2 is the actual AFOS battle:
part 1:
(The volume is a bit loud in part 2, you may want to turn down your speakers a bit. Sorry I messed up)
part 2:
As you can see in the videos, even though I kept the booster pack in the first half, it got removed in the second half. I'm not sure if this happens in all chronicle missions or just in this particular one.
@~Homer~likeVF19A Thanks, that's really helpful!