Problem:
I was trying to save and load the SkulkerBoxes BlockState from my own serialized data (foreign to Spigot) and I noticed that I was not able to modify the BlockState and thus the inventory of the ShulkerBox while it was not placed.

We'd need to override #update and save the nbt data of ShulkerBoxes to allow modification while the ShulkerBox is an item.

Possible Solution:
Upon digging, a similar problem was posed with Shields and fixed through overriding the update method here. The same strategy could be applied to ShulkerBoxes.

Thank you for reading and hopefull a quick resolving of this issue.