Update: the server owner has informed me that the server runs on a Paper jar, and this is an issue with Paper, not vanilla Minecraft.

Enchantments on an item will rearrange their order to copy another item with the same enchantments. This item was on the player recently, but the bug has also happened while the item being "copied" was in a shulker in the player's ender chest. 

Example: Fully enchanted diamond boots the player created recently were checked after being put in a shulker and taken out, and the enchantments had swapped places to match the order of enchantments on the player's worn Netherite boots (the items had the same enchantments before, but in a different order.) 

I don't know how to reproduce this, but it has happened multiple times, for multiple items. It doesn't appear to be nbt duplication either, as a "cloned" item did not inherit the name of the first item. 

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Image 1: A newly-enchanted pair of boots I made in creative with books and an anvil to test.

Image 2: The same pair of boots after a few minutes afk. The enchantments have changed order.

Image 3: The pair of boots I've had for a while. Their order was taken on by the boots in image 2.

Image 4: Another pair of boots I created recently (in survival), with the same enchantment order.

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I have more examples I can provide if needed, but that seems repetitive as it shows basically the exact same thing but on different items. 

I've only observed this bug happening with a Netherite item's enchantment order being copied by a Diamond item with the same enchantments.