This requires you have a stack upgrade and 2 containers that can store items via right clicking with the item to store. I specifically found this with the Tombstone Enchanted Bundles I found around the world, but I imagine any bag/storage that works similarly that can stack with the Sophisticated stack upgrade will do the same thing.

If the bundles are stacked in the inventory, you can add an item to the stack, then separate them and each will show as having the item you added to the stack's inventory.

Example: iron stack upgrade in a backpack + 2 enchanted bundles:

stack the enchanted bundles in the backpack

right click the ingot on the bundle stack

separate the bundle stack

nonStackableItems in the config can be used to define storage items like this one to not stack and prevent the issue

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