Can you recall when you deleted them? your game history shows you had a gap between 2017 and 2020 - if you deleted them back in 2017 then that was prior to Bungie tracking items for collections and so they wouldn't have been recorded as obtained.
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I actually just deleted those shells and half the stuff in my vault two weeks ago when I came back to the game. Which is why I’m confused to why it didn’t save. Currently my resources say 0/0 and my small rice cakes are still in my inventory but blacked out in the collection book.