So I was messing around with the "nbt-editing" in 1.16 via /loot replace and shulker box loot tables and I found that it will delete items in the crafting area and other parts of the inventory when replacing certain parts. For example: 

Replacing the armor.head slot deletes the whole crafting area.

Replacing the armor.feet slot deletes the whole crafting area and every remaining armor slot.

Replacing the offhand deletes every armor slot and the whole crafting area

And so on..

This causes many issues since you can't replace the crafting slots and you have to replace so much nbt every time you only want to replace a single slot.

I think that it tries to replace the following 26 slots since there is air in a shulker box and the game wants to use that too.
It could be fixed by maybe ignoring air while replacing the item.