Hi Eloumeloun,
Thank you for submitting a bug report on this issue. I’m sorry to hear you’re experiencing issues with crafting and trophies in your save.
This issue you mentioned is similar to another player’s report on the Story items no longer being craftable for them. Had you killed any other bosses before this issue occured or previously unlocked the story items in the crafting menu? Thank you also for sharing this video.
The team are aware of the issue with the binoculars and are investigating this also.
With regards to the lost items, were these in crates, on the ground or in your inventory? Any extra info about the lost items would be greatly appreciated.
Unfortunately I do not have any workarounds for this issue, but should the team suggest any, I will update a Known Issues report I have created here: [Known Issue][PS4/XB1] Crafting Menu Reset