if you lose essential/unique items, you can make a new story mode save to fetch them, and put them in the mailbox. When you save, the mailbox is saved to a different file that can be access by any other story mode mailbox, so anything that fits in your inventory can be sent between saves as needed. As for missing events and specific items... don't beat yourself up too much or stress about it, there is A LOT of minor events in the game and you will miss easily half of them to random chance alone. It makes playing through the game when it updates less boring and predictable