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It looks like when you complete a challenge that rewards atoms, your current atom balance temporarily resets to a different value. When you check the atomic shop, it reverts back to the original balance but you don't have those extra atoms that you were just rewarded. I suspect this only affects people who are on steam linked accounts.
So I did some thinking and checked my Bethesda account as I remember it tracked a separate atom balance from your steam linked account and lo and behold... There were my missing atoms.
Check it out yourself, log in to your Bethesda account and you will find the lost atoms just sitting there.
Edit #1: Another way to check your Bethesda client balance is as below (thanks /u/cmVkbmFz)
Or just use
bSteamEnabled=0 (1 for steam) In your Fallout76custom.ini
Edit #2: I couldn’t get the above setting to work but others have so your mileage may vary.
For reference here are some more posts about the topic: https://www.reddit.com/r/fo76/comments/huhnrd/atoms_keep_reverting_to_410_without_me_making/ https://www.reddit.com/r/fo76/comments/hu6hka/atoms_still_disappearing/ https://www.reddit.com/r/fo76/comments/gc0oqb/fallout_76_launches_through_steam_but_not_really/
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