When using a container that Quark interprets as a "Shulker box" which has more than 27 slots deletes all items that are not in the first three rows if an item is right click added to it in the inventory (and one of the first 27 slots is free)

(NOTE: I added Soul Urn to the list of things that get interpreted as shulker boxes)
In this example, if I were to pick up the soul urn and right click an item into it in my inventory, the rotten flesh would get voided

If you want to recreate it, I'd say test it with Iron Shulker Boxes