[Chaos]

Items received via the static Chests from the Loyrwell Tombs ('Above ground', not within the Crypt) do not seem to count towards crafting recipes, upgrades, certain events, etc. Additionally, these items do not stack with their normally-gained counterparts.

Within the spoiler is the list of items that aren't counted/don't stack normally, and which mechanics they aren't applying towards:

-Raremetal Shards (Does not count towards Equipment Upgrades)
-Chimeric Mass (Eyes gained from Mass do not count towards Potential Unlocks and Crafting Recipes)
-Black Pearls (Does not count towards Crafting Recipes)
-Dark Shards (Does not count towards accessing the 'Boss' of Loyrwell Tombs)