While I know about the idiocy that is the 10 minute cool down for getting faction tokens, you also said that it wouldn't affect other things. Well, you're wrong. I got absolutely nothing from completing the lost sector in Artifact's Edge. It was likely in this 10 minute cool down, but still got nothing else... no Nessus tokens... nothing, not even glimmer. Also did not get credit for the faction rally where you need to destroy supplies.
Good job... just when you think you can't screw up more, you go on and keep on surprising us.
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For the faction rally milestone, it’s not about opening the chest. It’s related to destroying the supply crate(s) throughout the Lost Sector. I just ran through multiple Lost Sectors (including the one in Artifact’s Edge multiple times & Exodus Black) to get into the cooldown lockout period, but I was still getting credits for destroying the crates from both sections during the lockout.
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You need to destroy crates in lost sectors on earth for the first milestone.