I never 'completed the quest'. I made the blocker, no update. I just decided to start a new quest with the bottan smugglers and when I got there I just used the blocker and had a new option in chat, destroy hyperdrive. I killed Bottan and was able to pick up the XSTN-K system upgrade, which was not visible. . At that point I got what I needed, but I never completed the quest or got any updates. As long as you have the system upgrade after the battle you can consider it done.