[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)

[K Peculier]

I can confirm that if you have chimeric eyes from the Loyrwell Tombs chest, getting anymore from other means via chimeric mass or chests do not count for it with the addition that you cannot delete the bugged eye, so a '1' chimeric eye is stuck in my inventory forever and cannot be added on.

[Neus]

These should be corrected. I also made an adjustment to the way the game looks up items to prefer to take the lowest cost version first in cases like these.