Items in bundle within bundle gone

Items in a bundle that are within another bundle disappear.

 

Situation:

I have a 8 bundles with items in them, some full, some partially full. Two of the bundles have partially filled bundles inside of them. (They are to be used as trick-or-treat bags for a Halloween build). All 8 bundles are inside an Shulker box, and that is inside an Ender Chest. I travel through the Nether to a different Overworld location to unpack them for the project. One of the partially filled bundles that was inside the others is now empty. I thought maybe I just forgot to pack it, so I go back through the Nether to the original location to get its contents. Now, the 2nd partially filled bundle that was inside a different bundle is empty. The other items (that are not bundles) are all still there. 

Another note is that all of the bundles have been dyed (assorted various colors) and renamed. (The now empty bundles were both renamed to "Colorful Cache" and before their contents disappeared, they each contained one dye of each color).

The items were not in my inventory while traversing the Nether, but remained in the Shulker box in the Ender Chest.