contents in bundles in shulker box disappeared

I put a bunch of copper, iron and cooked food into bundles in my shulker box

I then mined my shulker box with a pickaxe

Picked it up and few ~2500 clicks

placed my shulker box back at my main base

when I go to look in it, only my bundles that had copper were still full

all my other bundles were Empty!