It’s the same with scriptures, medipacks and ammo crates.
I’ve reported this problem here:
https://forums.fatsharkgames.com/t/merging-2-scriptures-into-1-but-still-counts-toward-melk-contracts-and-mission-end-rewards/90173/2
Seems it was not fixed (scripture merging is still a thing).
Edit: In case of scriptures it’s an exploit (still counts for progress and rewards) in case of rest it’s a bug - you can’t use other consumable that “disappeared”,