My objective was to get the 'Final Warning' weapon yet when I was attempting the 'The Final Strand - Defeat the Shadow Legion looters and read their orders to learn where they took the spoils' mission, I defeated the shadow legion and got their orders but the mission did not update.
How to recreate this issue:
Instead of taking the portal directly to the area for the mission, I took the long way around jumping over buildings till I got to the area. The enemies had exotic engrams above their heads. I defeated all of them and then went for the boss. When the boss was defeated the 'Shadow Legion Orders' loot was added to my inventory but the quest did not update.
I left the enemy area and basically restarted the mission and the same things happened but this time, after defeating the boss, the new 'Shadow Legion Orders' could not be put into the inventory. I then removed the 'Shadow Legion Orders' in my inventory and picked up the new 'Shadow Legion Orders' yet once again my quest did not update.
This occurred at 1:50 AM EST, on Tuesday, March 19 2024.
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In today's patch notes under "Bounties and Pursuits" it says: "- Fixed an issue where collecting the Cabal Missive did not advance The Final Strand quest. Collecting the Cabal Missive will now advance the quest." I can confirm it is still not working for me at least. I just posted a thread about it myself and have been watching this issue for several weeks.